HEADER HYDROLASE/HYDROLASE INHIBITOR 14-SEP-12 4H3X
TITLE CRYSTAL STRUCTURE OF AN MMP BROAD SPECTRUM HYDROXAMATE BASED INHIBITOR
TITLE 2 CC27 IN COMPLEX WITH THE MMP-9 CATALYTIC DOMAIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: MATRIX METALLOPROTEINASE-9;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: HUMAN WILD-TYPE MMP-9 CATALYTIC DOMAIN UNP RESIDUES 107-
COMPND 5 215/391-443;
COMPND 6 SYNONYM: MMP-9,92 KDA GELATINASE,92 KDA TYPE IV COLLAGENASE,
COMPND 7 GELATINASE B,GELB;
COMPND 8 EC: 3.4.24.35,3.4.24.35;
COMPND 9 ENGINEERED: YES;
COMPND 10 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: MMP9, CLG4B;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3 STAR);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PT7 PROMOTER;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-14B
KEYWDS HYDROLASE/HYDROXAMATE INHIBITOR, ZINCIN-LIKE, GELATINASE, COLLAGENASE
KEYWDS 2 (CATALYTIC DOMAIN), HYDROLASE-HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR E.A.STURA,L.VERA,E.CASSAR-LAJEUNESSE,E.NUTI,V.DIVE,A.ROSSELLO
REVDAT 6 20-SEP-23 4H3X 1 REMARK LINK
REVDAT 5 31-MAY-17 4H3X 1 COMPND REMARK DBREF
REVDAT 4 12-AUG-15 4H3X 1 JRNL
REVDAT 3 08-OCT-14 4H3X 1 AUTHOR
REVDAT 2 01-MAY-13 4H3X 1 AUTHOR
REVDAT 1 24-APR-13 4H3X 0
JRNL AUTH C.ANTONI,L.VERA,L.DEVEL,M.P.CATALANI,B.CZARNY,
JRNL AUTH 2 E.CASSAR-LAJEUNESSE,E.NUTI,A.ROSSELLO,V.DIVE,E.A.STURA
JRNL TITL CRYSTALLIZATION OF BI-FUNCTIONAL LIGAND PROTEIN COMPLEXES.
JRNL REF J.STRUCT.BIOL. V. 182 246 2013
JRNL REFN ISSN 1047-8477
JRNL PMID 23567804
JRNL DOI 10.1016/J.JSB.2013.03.015
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH C.ANTONI,L.VERA,L.DEVEL,M.P.CATALANI,B.CZARNY,
REMARK 1 AUTH 2 E.CASSAR-LAJEUNESSE,E.NUTI,A.ROSSELLO,V.DIVE,E.A.STURA
REMARK 1 TITL CRYSTALLIZATION OF BI-FUNCTIONAL LIGAND PROTEIN COMPLEXES.
REMARK 1 REF J.STRUCT.BIOL. 2013
REMARK 1 REFN ESSN 1095-8657
REMARK 1 PMID 23567804
REMARK 1 DOI 10.1016/J.JSB.2013.03.015
REMARK 2
REMARK 2 RESOLUTION. 1.76 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.76
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.81
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3
REMARK 3 NUMBER OF REFLECTIONS : 31949
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.199
REMARK 3 R VALUE (WORKING SET) : 0.196
REMARK 3 FREE R VALUE : 0.254
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1598
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 42.8181 - 3.9226 1.00 2837 150 0.1892 0.2333
REMARK 3 2 3.9226 - 3.1138 1.00 2807 148 0.1764 0.2212
REMARK 3 3 3.1138 - 2.7203 0.99 2776 146 0.1961 0.2836
REMARK 3 4 2.7203 - 2.4716 0.99 2789 146 0.1991 0.2359
REMARK 3 5 2.4716 - 2.2944 0.99 2762 146 0.1969 0.3139
REMARK 3 6 2.2944 - 2.1592 0.99 2788 147 0.1984 0.2603
REMARK 3 7 2.1592 - 2.0510 0.99 2769 145 0.1875 0.2380
REMARK 3 8 2.0510 - 1.9618 0.98 2748 145 0.2000 0.2444
REMARK 3 9 1.9618 - 1.8862 0.99 2754 145 0.2077 0.2585
REMARK 3 10 1.8862 - 1.8211 0.98 2723 143 0.2343 0.3088
REMARK 3 11 1.8211 - 1.7642 0.92 2598 137 0.2696 0.3117
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.490
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 24.44
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.007 2957
REMARK 3 ANGLE : 1.030 4030
REMARK 3 CHIRALITY : 0.074 385
REMARK 3 PLANARITY : 0.006 533
REMARK 3 DIHEDRAL : 18.451 1069
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 4H3X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-SEP-12.
REMARK 100 THE DEPOSITION ID IS D_1000074987.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 31-JAN-11
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID23-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726
REMARK 200 MONOCHROMATOR : HORIZONTALLY DIFFRACTING SI
REMARK 200 (111) MONOCHROMATOR AND PT
REMARK 200 COATED MIRRORS IN KIRKPATRICK-
REMARK 200 BAEZ GEOMETRY FOR FOCUSING
REMARK 200 OPTICS : BENT CYLINDRICAL MIRROR
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31957
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0
REMARK 200 DATA REDUNDANCY : 4.230
REMARK 200 R MERGE (I) : 0.13600
REMARK 200 R SYM (I) : 0.11900
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.4100
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87
REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2
REMARK 200 DATA REDUNDANCY IN SHELL : 4.13
REMARK 200 R MERGE FOR SHELL (I) : 0.66600
REMARK 200 R SYM FOR SHELL (I) : 0.58200
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.330
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: 4H2E
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.34
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: HMMP-9-WT 5.5 MG/ML 120 MILLI
REMARK 280 -M ACETOHYDROXAMIC ACID. RESERVOIR: 10% PEG 20,000, 60MM MES PH
REMARK 280 5.5 + 18% MPEG 5,000, 0.08 M IMIDAZOLE PIPERIDINE; PH 8.5, 0.05
REMARK 280 M NACL. CRYOPROTECTANT: 10% DI-ETHYLENE GLYCOL, 10% 1.2-
REMARK 280 PROPANEDIOL, 10% GLYCEROL, 10% PEG 10K, 10% PCTP 50/50, 200MM
REMARK 280 NACL , VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, PH 7.0
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 48.97000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 ALA A 173 -136.51 46.04
REMARK 500 ASP A 185 -168.07 65.44
REMARK 500 PRO A 246 48.68 -83.44
REMARK 500 PRO A 246 48.87 -83.44
REMARK 500 ALA B 173 -141.01 57.61
REMARK 500 ASP B 185 -166.37 62.72
REMARK 500 PRO B 246 49.34 -75.82
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 552 DISTANCE = 6.11 ANGSTROMS
REMARK 525 HOH B 474 DISTANCE = 7.22 ANGSTROMS
REMARK 525 HOH B 510 DISTANCE = 6.01 ANGSTROMS
REMARK 525 HOH B 555 DISTANCE = 6.43 ANGSTROMS
REMARK 525 HOH B 557 DISTANCE = 8.04 ANGSTROMS
REMARK 525 HOH B 558 DISTANCE = 6.75 ANGSTROMS
REMARK 525 HOH B 562 DISTANCE = 6.76 ANGSTROMS
REMARK 525 HOH B 570 DISTANCE = 6.14 ANGSTROMS
REMARK 525 HOH B 580 DISTANCE = 6.46 ANGSTROMS
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 304 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 131 OD2
REMARK 620 2 ASP A 131 OD1 48.1
REMARK 620 3 ASP A 206 O 154.4 150.8
REMARK 620 4 ASP A 206 OD1 89.7 95.9 73.9
REMARK 620 5 GLU A 208 O 81.6 122.2 86.7 112.5
REMARK 620 6 HOH A 452 O 122.7 77.0 74.3 79.7 153.8
REMARK 620 7 HOH A 453 O 100.5 84.3 99.4 166.2 78.4 86.9
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 305 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 165 O
REMARK 620 2 GLY A 197 O 171.0
REMARK 620 3 GLN A 199 O 105.0 84.0
REMARK 620 4 ASP A 201 OD1 89.0 90.6 93.9
REMARK 620 5 HOH A 406 O 87.7 83.4 165.2 94.0
REMARK 620 6 HOH A 411 O 90.0 91.2 81.4 174.8 91.0
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 302 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 175 NE2
REMARK 620 2 ASP A 177 OD1 115.8
REMARK 620 3 HIS A 190 NE2 115.1 113.6
REMARK 620 4 HIS A 203 ND1 107.1 91.7 110.7
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 303 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 182 OD1
REMARK 620 2 GLY A 183 O 87.1
REMARK 620 3 ASP A 185 O 88.7 87.5
REMARK 620 4 LEU A 187 O 94.7 178.2 92.7
REMARK 620 5 ASP A 205 OD2 93.2 89.8 176.7 89.9
REMARK 620 6 GLU A 208 OE2 165.0 82.6 80.0 95.7 97.7
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 301 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 226 NE2
REMARK 620 2 HIS A 230 NE2 95.3
REMARK 620 3 HIS A 236 NE2 104.7 91.8
REMARK 620 4 10B A 306 O7 99.1 94.9 154.5
REMARK 620 5 10B A 306 O2 152.3 111.9 80.9 73.8
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA B 304 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 131 OD2
REMARK 620 2 ASP B 131 OD1 48.4
REMARK 620 3 ASP B 206 O 153.3 148.6
REMARK 620 4 ASP B 206 OD1 92.3 94.7 69.8
REMARK 620 5 GLU B 208 O 78.3 123.6 87.4 105.6
REMARK 620 6 HOH B 468 O 104.9 58.8 90.5 76.7 176.1
REMARK 620 7 HOH B 529 O 107.6 88.2 95.4 155.2 93.0 83.9
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA B 305 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 165 O
REMARK 620 2 GLY B 197 O 168.6
REMARK 620 3 GLN B 199 O 105.0 86.2
REMARK 620 4 ASP B 201 OD1 89.6 90.4 100.1
REMARK 620 5 HOH B 401 O 86.7 94.5 74.8 172.6
REMARK 620 6 HOH B 405 O 90.2 78.4 159.7 93.3 93.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 302 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS B 175 NE2
REMARK 620 2 ASP B 177 OD1 118.2
REMARK 620 3 HIS B 190 NE2 105.6 112.0
REMARK 620 4 HIS B 203 ND1 115.6 95.8 109.4
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA B 303 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 182 OD1
REMARK 620 2 GLY B 183 O 89.3
REMARK 620 3 ASP B 185 O 82.7 84.0
REMARK 620 4 LEU B 187 O 95.0 175.1 94.3
REMARK 620 5 ASP B 205 OD2 90.9 92.1 172.6 90.0
REMARK 620 6 GLU B 208 OE2 165.5 90.5 82.8 84.8 103.6
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 301 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS B 226 NE2
REMARK 620 2 HIS B 230 NE2 93.7
REMARK 620 3 HIS B 236 NE2 105.0 96.3
REMARK 620 4 10B B 306 O2 134.4 130.8 82.4
REMARK 620 5 10B B 306 O7 98.1 96.3 152.8 71.1
REMARK 620 N 1 2 3 4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 304
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 10B A 306
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 307
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 308
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 309
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGO A 310
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 311
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 312
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 313
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 304
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 305
REMARK 800
REMARK 800 SITE_IDENTIFIER: CC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 10B B 306
REMARK 800
REMARK 800 SITE_IDENTIFIER: CC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 307
REMARK 800
REMARK 800 SITE_IDENTIFIER: CC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 308
REMARK 800
REMARK 800 SITE_IDENTIFIER: CC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 309
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4H1Q RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF MUTANT MMP-9 CATALYTIC DOMAIN IN COMPLEX WITH
REMARK 900 A TWIN INHIBITOR.
REMARK 900 RELATED ID: 4H2E RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF AN MMP TWIN INHIBITOR COMPLEXING TWO MMP-9
REMARK 900 CATALYTIC DOMAINS
REMARK 900 RELATED ID: 2OW1 RELATED DB: PDB
REMARK 900 MMP-9 ACTIVE SITE MUTANT WITH TRIFLUOROMETHYL HYDROXAMATE INHIBITOR
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 THE CRYSTALLIZED SEQUENCE CORRESPONDS TO A CHIMERIC CONSTRUCT
REMARK 999 OBTAINED BY DELETING THE DOMAIN CORRESPONDING TO UNP RESIDUES 215-
REMARK 999 390
DBREF 4H3X A 107 216 UNP P14780 MMP9_HUMAN 107 216
DBREF 4H3X A 217 269 UNP P14780 MMP9_HUMAN 392 444
DBREF 4H3X B 107 216 UNP P14780 MMP9_HUMAN 107 216
DBREF 4H3X B 217 269 UNP P14780 MMP9_HUMAN 392 444
SEQADV 4H3X GLY A 106 UNP P14780 EXPRESSION TAG
SEQADV 4H3X GLY B 106 UNP P14780 EXPRESSION TAG
SEQRES 1 A 164 GLY PHE GLN THR PHE GLU GLY ASP LEU LYS TRP HIS HIS
SEQRES 2 A 164 HIS ASN ILE THR TYR TRP ILE GLN ASN TYR SER GLU ASP
SEQRES 3 A 164 LEU PRO ARG ALA VAL ILE ASP ASP ALA PHE ALA ARG ALA
SEQRES 4 A 164 PHE ALA LEU TRP SER ALA VAL THR PRO LEU THR PHE THR
SEQRES 5 A 164 ARG VAL TYR SER ARG ASP ALA ASP ILE VAL ILE GLN PHE
SEQRES 6 A 164 GLY VAL ALA GLU HIS GLY ASP GLY TYR PRO PHE ASP GLY
SEQRES 7 A 164 LYS ASP GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO
SEQRES 8 A 164 GLY ILE GLN GLY ASP ALA HIS PHE ASP ASP ASP GLU LEU
SEQRES 9 A 164 TRP SER LEU GLY LYS GLY VAL GLY TYR SER LEU PHE LEU
SEQRES 10 A 164 VAL ALA ALA HIS GLU PHE GLY HIS ALA LEU GLY LEU ASP
SEQRES 11 A 164 HIS SER SER VAL PRO GLU ALA LEU MET TYR PRO MET TYR
SEQRES 12 A 164 ARG PHE THR GLU GLY PRO PRO LEU HIS LYS ASP ASP VAL
SEQRES 13 A 164 ASN GLY ILE ARG HIS LEU TYR GLY
SEQRES 1 B 164 GLY PHE GLN THR PHE GLU GLY ASP LEU LYS TRP HIS HIS
SEQRES 2 B 164 HIS ASN ILE THR TYR TRP ILE GLN ASN TYR SER GLU ASP
SEQRES 3 B 164 LEU PRO ARG ALA VAL ILE ASP ASP ALA PHE ALA ARG ALA
SEQRES 4 B 164 PHE ALA LEU TRP SER ALA VAL THR PRO LEU THR PHE THR
SEQRES 5 B 164 ARG VAL TYR SER ARG ASP ALA ASP ILE VAL ILE GLN PHE
SEQRES 6 B 164 GLY VAL ALA GLU HIS GLY ASP GLY TYR PRO PHE ASP GLY
SEQRES 7 B 164 LYS ASP GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO
SEQRES 8 B 164 GLY ILE GLN GLY ASP ALA HIS PHE ASP ASP ASP GLU LEU
SEQRES 9 B 164 TRP SER LEU GLY LYS GLY VAL GLY TYR SER LEU PHE LEU
SEQRES 10 B 164 VAL ALA ALA HIS GLU PHE GLY HIS ALA LEU GLY LEU ASP
SEQRES 11 B 164 HIS SER SER VAL PRO GLU ALA LEU MET TYR PRO MET TYR
SEQRES 12 B 164 ARG PHE THR GLU GLY PRO PRO LEU HIS LYS ASP ASP VAL
SEQRES 13 B 164 ASN GLY ILE ARG HIS LEU TYR GLY
HET ZN A 301 1
HET ZN A 302 1
HET CA A 303 1
HET CA A 304 1
HET CA A 305 1
HET 10B A 306 25
HET GOL A 307 6
HET GOL A 308 6
HET GOL A 309 6
HET PGO A 310 5
HET GOL A 311 6
HET GOL A 312 6
HET GOL A 313 6
HET ZN B 301 1
HET ZN B 302 1
HET CA B 303 1
HET CA B 304 1
HET CA B 305 1
HET 10B B 306 25
HET GOL B 307 6
HET PEG B 308 7
HET PEG B 309 7
HETNAM ZN ZINC ION
HETNAM CA CALCIUM ION
HETNAM 10B N-2-(BIPHENYL-4-YLSULFONYL)-N-2-(ISOPROPYLOXY)-
HETNAM 2 10B ACETOHYDROXAMIC ACID
HETNAM GOL GLYCEROL
HETNAM PGO S-1,2-PROPANEDIOL
HETNAM PEG DI(HYDROXYETHYL)ETHER
HETSYN 10B N~2~-(BIPHENYL-4-YLSULFONYL)-N-HYDROXY-N~2~-(PROPAN-2-
HETSYN 2 10B YLOXY)GLYCINAMIDE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 3 ZN 4(ZN 2+)
FORMUL 5 CA 6(CA 2+)
FORMUL 8 10B 2(C17 H20 N2 O5 S)
FORMUL 9 GOL 7(C3 H8 O3)
FORMUL 12 PGO C3 H8 O2
FORMUL 23 PEG 2(C4 H10 O3)
FORMUL 25 HOH *380(H2 O)
HELIX 1 1 PRO A 133 VAL A 151 1 19
HELIX 2 2 LEU A 220 LEU A 232 1 13
HELIX 3 3 HIS A 257 GLY A 269 1 13
HELIX 4 4 PRO B 133 ALA B 150 1 18
HELIX 5 5 LEU B 220 GLY B 233 1 14
HELIX 6 6 HIS B 257 GLY B 269 1 13
SHEET 1 A 2 GLN A 108 THR A 109 0
SHEET 2 A 2 LEU A 234 ASP A 235 -1 O ASP A 235 N GLN A 108
SHEET 1 B 5 THR A 155 ARG A 158 0
SHEET 2 B 5 ASN A 120 ILE A 125 1 N ILE A 121 O THR A 157
SHEET 3 B 5 ILE A 166 GLY A 171 1 O ILE A 168 N TRP A 124
SHEET 4 B 5 ALA A 202 ASP A 205 1 O PHE A 204 N GLN A 169
SHEET 5 B 5 ALA A 189 ALA A 191 -1 N HIS A 190 O HIS A 203
SHEET 1 C 2 TRP A 210 SER A 211 0
SHEET 2 C 2 TYR A 218 SER A 219 1 O TYR A 218 N SER A 211
SHEET 1 D 5 THR B 155 ARG B 158 0
SHEET 2 D 5 ASN B 120 ILE B 125 1 N ILE B 121 O THR B 157
SHEET 3 D 5 ILE B 166 GLY B 171 1 O ILE B 168 N TRP B 124
SHEET 4 D 5 ALA B 202 ASP B 205 1 O PHE B 204 N GLN B 169
SHEET 5 D 5 ALA B 189 ALA B 191 -1 N HIS B 190 O HIS B 203
SHEET 1 E 2 TRP B 210 SER B 211 0
SHEET 2 E 2 TYR B 218 SER B 219 1 O TYR B 218 N SER B 211
LINK OD2 ASP A 131 CA CA A 304 1555 1555 2.33
LINK OD1 ASP A 131 CA CA A 304 1555 1555 2.90
LINK O ASP A 165 CA CA A 305 1555 1555 2.32
LINK NE2 HIS A 175 ZN ZN A 302 1555 1555 2.16
LINK OD1 ASP A 177 ZN ZN A 302 1555 1555 2.02
LINK OD1 ASP A 182 CA CA A 303 1555 1555 2.31
LINK O GLY A 183 CA CA A 303 1555 1555 2.26
LINK O ASP A 185 CA CA A 303 1555 1555 2.34
LINK O LEU A 187 CA CA A 303 1555 1555 2.34
LINK NE2 HIS A 190 ZN ZN A 302 1555 1555 1.95
LINK O GLY A 197 CA CA A 305 1555 1555 2.33
LINK O GLN A 199 CA CA A 305 1555 1555 2.35
LINK OD1 ASP A 201 CA CA A 305 1555 1555 2.35
LINK ND1 HIS A 203 ZN ZN A 302 1555 1555 2.01
LINK OD2 ASP A 205 CA CA A 303 1555 1555 2.24
LINK O ASP A 206 CA CA A 304 1555 1555 2.30
LINK OD1 ASP A 206 CA CA A 304 1555 1555 2.41
LINK OE2 GLU A 208 CA CA A 303 1555 1555 2.25
LINK O GLU A 208 CA CA A 304 1555 1555 2.35
LINK NE2 HIS A 226 ZN ZN A 301 1555 1555 1.97
LINK NE2 HIS A 230 ZN ZN A 301 1555 1555 2.12
LINK NE2 HIS A 236 ZN ZN A 301 1555 1555 2.21
LINK ZN ZN A 301 O7 10B A 306 1555 1555 2.01
LINK ZN ZN A 301 O2 10B A 306 1555 1555 2.36
LINK CA CA A 304 O HOH A 452 1555 1555 2.51
LINK CA CA A 304 O HOH A 453 1555 1555 2.40
LINK CA CA A 305 O HOH A 406 1555 1555 2.43
LINK CA CA A 305 O HOH A 411 1555 1555 2.34
LINK OD2 ASP B 131 CA CA B 304 1555 1555 2.36
LINK OD1 ASP B 131 CA CA B 304 1555 1555 2.87
LINK O ASP B 165 CA CA B 305 1555 1555 2.33
LINK NE2 HIS B 175 ZN ZN B 302 1555 1555 2.11
LINK OD1 ASP B 177 ZN ZN B 302 1555 1555 1.96
LINK OD1 ASP B 182 CA CA B 303 1555 1555 2.42
LINK O GLY B 183 CA CA B 303 1555 1555 2.32
LINK O ASP B 185 CA CA B 303 1555 1555 2.42
LINK O LEU B 187 CA CA B 303 1555 1555 2.31
LINK NE2 HIS B 190 ZN ZN B 302 1555 1555 2.10
LINK O GLY B 197 CA CA B 305 1555 1555 2.47
LINK O GLN B 199 CA CA B 305 1555 1555 2.44
LINK OD1 ASP B 201 CA CA B 305 1555 1555 2.41
LINK ND1 HIS B 203 ZN ZN B 302 1555 1555 2.04
LINK OD2 ASP B 205 CA CA B 303 1555 1555 2.31
LINK O ASP B 206 CA CA B 304 1555 1555 2.43
LINK OD1 ASP B 206 CA CA B 304 1555 1555 2.47
LINK OE2 GLU B 208 CA CA B 303 1555 1555 2.21
LINK O GLU B 208 CA CA B 304 1555 1555 2.40
LINK NE2 HIS B 226 ZN ZN B 301 1555 1555 2.13
LINK NE2 HIS B 230 ZN ZN B 301 1555 1555 2.09
LINK NE2 HIS B 236 ZN ZN B 301 1555 1555 2.09
LINK ZN ZN B 301 O2 10B B 306 1555 1555 2.20
LINK ZN ZN B 301 O7 10B B 306 1555 1555 2.30
LINK CA CA B 304 O HOH B 468 1555 1555 2.48
LINK CA CA B 304 O HOH B 529 1555 1555 2.49
LINK CA CA B 305 O HOH B 401 1555 1555 2.26
LINK CA CA B 305 O HOH B 405 1555 1555 2.41
SITE 1 AC1 4 HIS A 226 HIS A 230 HIS A 236 10B A 306
SITE 1 AC2 4 HIS A 175 ASP A 177 HIS A 190 HIS A 203
SITE 1 AC3 6 ASP A 182 GLY A 183 ASP A 185 LEU A 187
SITE 2 AC3 6 ASP A 205 GLU A 208
SITE 1 AC4 5 ASP A 131 ASP A 206 GLU A 208 HOH A 452
SITE 2 AC4 5 HOH A 453
SITE 1 AC5 6 ASP A 165 GLY A 197 GLN A 199 ASP A 201
SITE 2 AC5 6 HOH A 406 HOH A 411
SITE 1 AC6 17 GLY A 186 LEU A 187 LEU A 188 ALA A 189
SITE 2 AC6 17 LEU A 222 HIS A 226 GLU A 227 HIS A 230
SITE 3 AC6 17 HIS A 236 LEU A 243 TYR A 245 MET A 247
SITE 4 AC6 17 ZN A 301 HOH A 415 HOH A 492 TYR B 245
SITE 5 AC6 17 PRO B 246
SITE 1 AC7 6 PRO A 254 HOH A 421 PRO B 254 PRO B 255
SITE 2 AC7 6 HOH B 448 HOH B 451
SITE 1 AC8 9 ASP A 177 GLY A 178 GOL A 311 HOH A 476
SITE 2 AC8 9 HOH A 515 HOH A 553 HOH A 559 HOH A 560
SITE 3 AC8 9 HOH A 590
SITE 1 AC9 7 TYR A 179 LEU A 187 HIS A 190 HOH A 594
SITE 2 AC9 7 HOH A 595 PRO B 240 TYR B 245
SITE 1 BC1 2 ALA A 173 GLU A 174
SITE 1 BC2 5 GOL A 308 HOH A 480 HOH A 515 HOH A 529
SITE 2 BC2 5 HOH A 553
SITE 1 BC3 4 ASN A 120 THR A 122 THR A 157 HOH A 536
SITE 1 BC4 2 HOH A 434 HOH A 483
SITE 1 BC5 4 HIS B 226 HIS B 230 HIS B 236 10B B 306
SITE 1 BC6 4 HIS B 175 ASP B 177 HIS B 190 HIS B 203
SITE 1 BC7 6 ASP B 182 GLY B 183 ASP B 185 LEU B 187
SITE 2 BC7 6 ASP B 205 GLU B 208
SITE 1 BC8 5 ASP B 131 ASP B 206 GLU B 208 HOH B 468
SITE 2 BC8 5 HOH B 529
SITE 1 BC9 6 ASP B 165 GLY B 197 GLN B 199 ASP B 201
SITE 2 BC9 6 HOH B 401 HOH B 405
SITE 1 CC1 18 TYR A 245 PRO A 246 MET A 247 GLY B 186
SITE 2 CC1 18 LEU B 187 LEU B 188 ALA B 189 LEU B 222
SITE 3 CC1 18 HIS B 226 GLU B 227 HIS B 230 HIS B 236
SITE 4 CC1 18 LEU B 243 TYR B 245 MET B 247 TYR B 248
SITE 5 CC1 18 ZN B 301 HOH B 444
SITE 1 CC2 5 PHE B 250 THR B 251 HOH B 423 HOH B 515
SITE 2 CC2 5 HOH B 546
SITE 1 CC3 4 PEG B 309 HOH B 442 HOH B 443 HOH B 480
SITE 1 CC4 3 TYR B 179 PEG B 308 HOH B 442
CRYST1 40.110 97.940 46.080 90.00 111.73 90.00 P 1 21 1 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.024931 0.000000 0.009937 0.00000
SCALE2 0.000000 0.010210 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023361 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
