HEADER HYDROLASE 26-OCT-04 1XUR
TITLE MATRIX METALLOPROTEINASE-13 COMPLEXED WITH NON-ZINC BINDING INHIBITOR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: COLLAGENASE 3;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: CATALYTIC DOMAIN;
COMPND 5 SYNONYM: MATRIX METALLOPROTEINASE-13, MMP-13;
COMPND 6 EC: 3.4.24.-;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS MATRIX METALLOPROTEINASE, NON-ZINC BINDING INHIBITOR, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR C.K.ENGEL,K.U.WENDT
REVDAT 3 13-MAR-24 1XUR 1 REMARK LINK
REVDAT 2 24-FEB-09 1XUR 1 VERSN
REVDAT 1 26-OCT-05 1XUR 0
JRNL AUTH C.K.ENGEL,B.PIRARD,S.SCHIMANSKI,R.KIRSCH,J.HABERMANN,
JRNL AUTH 2 O.KLINGLER,V.SCHLOTTE,K.U.WEITHMANN,K.U.WENDT
JRNL TITL STRUCTURAL BASIS FOR THE HIGHLY SELECTIVE INHIBITION OF
JRNL TITL 2 MMP-13.
JRNL REF CHEM.BIOL. V. 12 181 2005
JRNL REFN ISSN 1074-5521
JRNL PMID 15734640
JRNL DOI 10.1016/J.CHEMBIOL.2004.11.014
REMARK 2
REMARK 2 RESOLUTION. 1.85 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.4
REMARK 3 NUMBER OF REFLECTIONS : 30251
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : FROM RFREE MASTER FILE
REMARK 3 R VALUE (WORKING SET) : 0.167
REMARK 3 FREE R VALUE : 0.206
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.900
REMARK 3 FREE R VALUE TEST SET COUNT : 2726
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2667
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 60
REMARK 3 SOLVENT ATOMS : 505
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 16.60
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.00100
REMARK 3 B22 (A**2) : 0.00700
REMARK 3 B33 (A**2) : -0.00800
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.02700
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : NULL
REMARK 3 BOND ANGLES (DEGREES) : NULL
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : NULL
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1XUR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-OCT-04.
REMARK 100 THE DEPOSITION ID IS D_1000030785.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID14-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.934
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30251
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4
REMARK 200 DATA REDUNDANCY : 3.500
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.03500
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.3600
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90
REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0
REMARK 200 DATA REDUNDANCY IN SHELL : 2.70
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.07100
REMARK 200 <I/SIGMA(I)> FOR SHELL : 10.71
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: CNS
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.88
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
REMARK 290 4555 -X+1/2,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 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 67.25400
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.24300
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.25400
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.24300
REMARK 290 SMTRY3 4 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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 4420 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 16490 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -115.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 11820 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 29990 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -240.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 10.29337
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 145.31848
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 PRO A 273
REMARK 465 ASN A 274
REMARK 465 ASP B 270
REMARK 465 GLU B 271
REMARK 465 ASP B 272
REMARK 465 PRO B 273
REMARK 465 ASN B 274
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH B 3108 O HOH B 3108 2657 1.01
REMARK 500
REMARK 500 REMARK: NULL
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 LYS A 170 -131.03 41.53
REMARK 500 SER A 182 172.60 74.47
REMARK 500 ASN A 194 -112.55 49.81
REMARK 500 SER A 210 -151.63 -118.00
REMARK 500 LYS B 170 -134.95 43.21
REMARK 500 SER B 182 171.65 69.02
REMARK 500 ALA B 186 171.46 178.50
REMARK 500 ASN B 194 -120.46 55.17
REMARK 500 SER B 211 -146.00 -127.84
REMARK 500
REMARK 500 REMARK: NULL
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 A1265 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 162 O
REMARK 620 2 ASN A 194 O 156.7
REMARK 620 3 GLY A 196 O 83.6 95.8
REMARK 620 4 ASP A 198 OD1 90.9 112.2 98.1
REMARK 620 5 HOH A2104 O 97.0 77.9 165.5 96.4
REMARK 620 6 HOH A2116 O 88.0 69.5 74.7 172.8 90.9
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A1262 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 172 NE2
REMARK 620 2 ASP A 174 OD2 108.0
REMARK 620 3 HIS A 187 NE2 117.8 117.8
REMARK 620 4 HIS A 200 ND1 107.0 93.7 109.4
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A1264 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 179 OD1
REMARK 620 2 GLY A 180 O 86.1
REMARK 620 3 SER A 182 O 78.6 81.1
REMARK 620 4 LEU A 184 O 95.1 177.3 96.8
REMARK 620 5 ASP A 202 OD2 94.0 91.8 170.0 90.5
REMARK 620 6 GLU A 205 OE2 160.9 83.0 84.2 95.2 101.9
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A1261 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 222 NE2
REMARK 620 2 HIS A 226 NE2 97.9
REMARK 620 3 HIS A 232 NE2 110.6 99.0
REMARK 620 4 HOH A2016 O 80.3 177.2 83.6
REMARK 620 5 HOH A2023 O 111.5 100.1 130.3 78.8
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA B1265 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 162 O
REMARK 620 2 ASN B 194 O 166.5
REMARK 620 3 GLY B 196 O 82.8 94.3
REMARK 620 4 ASP B 198 OD1 90.9 102.5 97.9
REMARK 620 5 HOH B3077 O 80.5 86.1 72.6 167.8
REMARK 620 6 HOH B3137 O 103.1 76.4 163.6 97.3 93.1
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B1262 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS B 172 NE2
REMARK 620 2 ASP B 174 OD2 116.6
REMARK 620 3 HIS B 187 NE2 110.6 115.4
REMARK 620 4 HIS B 200 ND1 108.7 91.8 112.2
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA B1264 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 179 OD1
REMARK 620 2 GLY B 180 O 88.8
REMARK 620 3 SER B 182 O 77.4 81.1
REMARK 620 4 LEU B 184 O 94.0 176.8 101.0
REMARK 620 5 ASP B 202 OD2 93.1 86.8 164.7 91.5
REMARK 620 6 GLU B 205 OE2 155.5 70.9 85.8 106.7 99.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B1261 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS B 222 NE2
REMARK 620 2 HIS B 226 NE2 103.8
REMARK 620 3 HIS B 232 NE2 113.7 97.8
REMARK 620 4 HOH B3012 O 85.3 170.9 78.4
REMARK 620 5 HOH B3017 O 115.7 109.2 114.3 65.7
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 1261
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1262
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1264
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1265
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1261
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1262
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1264
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1265
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB5 A 2001
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB5 B 3001
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1XUC RELATED DB: PDB
REMARK 900 THE SAME PROTEIN WITH PB3
REMARK 900 RELATED ID: 1XUD RELATED DB: PDB
REMARK 900 THE SAME PROTEIN WITH PB4
DBREF 1XUR A 104 274 UNP P45452 MMP13_HUMAN 104 274
DBREF 1XUR B 104 274 UNP P45452 MMP13_HUMAN 104 274
SEQRES 1 A 171 TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER LYS MET
SEQRES 2 A 171 ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP MET
SEQRES 3 A 171 THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS ALA PHE
SEQRES 4 A 171 LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE THR ARG
SEQRES 5 A 171 LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER PHE GLY
SEQRES 6 A 171 ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO
SEQRES 7 A 171 SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO ASN
SEQRES 8 A 171 TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU THR TRP
SEQRES 9 A 171 THR SER SER SER LYS GLY TYR ASN LEU PHE LEU VAL ALA
SEQRES 10 A 171 ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP HIS SER
SEQRES 11 A 171 LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR THR TYR
SEQRES 12 A 171 THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP ASP VAL
SEQRES 13 A 171 GLN GLY ILE GLN SER LEU TYR GLY PRO GLY ASP GLU ASP
SEQRES 14 A 171 PRO ASN
SEQRES 1 B 171 TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER LYS MET
SEQRES 2 B 171 ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP MET
SEQRES 3 B 171 THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS ALA PHE
SEQRES 4 B 171 LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE THR ARG
SEQRES 5 B 171 LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER PHE GLY
SEQRES 6 B 171 ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO
SEQRES 7 B 171 SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO ASN
SEQRES 8 B 171 TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU THR TRP
SEQRES 9 B 171 THR SER SER SER LYS GLY TYR ASN LEU PHE LEU VAL ALA
SEQRES 10 B 171 ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP HIS SER
SEQRES 11 B 171 LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR THR TYR
SEQRES 12 B 171 THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP ASP VAL
SEQRES 13 B 171 GLN GLY ILE GLN SER LEU TYR GLY PRO GLY ASP GLU ASP
SEQRES 14 B 171 PRO ASN
HET ZN A1261 1
HET ZN A1262 1
HET CA A1264 1
HET CA A1265 1
HET PB5 A2001 26
HET ZN B1261 1
HET ZN B1262 1
HET CA B1264 1
HET CA B1265 1
HET PB5 B3001 26
HETNAM ZN ZINC ION
HETNAM CA CALCIUM ION
HETNAM PB5 N,N'-BIS(PYRIDIN-3-YLMETHYL)PYRIMIDINE-4,6-
HETNAM 2 PB5 DICARBOXAMIDE
HETSYN PB5 PYRIMIDINE-4,6-DICARBOXYLIC ACID BIS-[(PYRIDIN-3-
HETSYN 2 PB5 YLMETHYL)-AMIDE]
FORMUL 3 ZN 4(ZN 2+)
FORMUL 5 CA 4(CA 2+)
FORMUL 7 PB5 2(C18 H16 N6 O2)
FORMUL 13 HOH *505(H2 O)
HELIX 1 1 THR A 130 ASP A 147 1 18
HELIX 2 2 LEU A 216 GLY A 229 1 14
HELIX 3 3 PRO A 255 GLY A 267 1 13
HELIX 4 4 THR B 130 ASP B 147 1 18
HELIX 5 5 LEU B 216 LEU B 228 1 13
HELIX 6 6 PRO B 255 GLY B 267 1 13
SHEET 1 A 5 ASN A 152 LEU A 156 0
SHEET 2 A 5 ASN A 117 ILE A 122 1 N LEU A 118 O ASN A 152
SHEET 3 A 5 ILE A 163 GLY A 168 1 O ILE A 165 N ARG A 121
SHEET 4 A 5 ALA A 199 ASP A 202 1 O PHE A 201 N GLY A 168
SHEET 5 A 5 ALA A 186 ALA A 188 -1 N HIS A 187 O HIS A 200
SHEET 1 B 2 TRP A 207 THR A 208 0
SHEET 2 B 2 TYR A 214 ASN A 215 1 O TYR A 214 N THR A 208
SHEET 1 C 5 ASN B 152 ARG B 155 0
SHEET 2 C 5 ASN B 117 ILE B 122 1 N LEU B 118 O ASN B 152
SHEET 3 C 5 ILE B 163 GLY B 168 1 O ILE B 165 N ARG B 121
SHEET 4 C 5 ALA B 199 ASP B 202 1 O PHE B 201 N GLY B 168
SHEET 5 C 5 ALA B 186 ALA B 188 -1 N HIS B 187 O HIS B 200
SHEET 1 D 2 TRP B 207 THR B 208 0
SHEET 2 D 2 TYR B 214 ASN B 215 1 O TYR B 214 N THR B 208
LINK O ASP A 162 CA CA A1265 1555 1555 2.55
LINK NE2 HIS A 172 ZN ZN A1262 1555 1555 2.11
LINK OD2 ASP A 174 ZN ZN A1262 1555 1555 2.03
LINK OD1 ASP A 179 CA CA A1264 1555 1555 2.50
LINK O GLY A 180 CA CA A1264 1555 1555 2.44
LINK O SER A 182 CA CA A1264 1555 1555 2.55
LINK O LEU A 184 CA CA A1264 1555 1555 2.39
LINK NE2 HIS A 187 ZN ZN A1262 1555 1555 2.17
LINK O ASN A 194 CA CA A1265 1555 1555 2.51
LINK O GLY A 196 CA CA A1265 1555 1555 2.54
LINK OD1 ASP A 198 CA CA A1265 1555 1555 2.60
LINK ND1 HIS A 200 ZN ZN A1262 1555 1555 2.14
LINK OD2 ASP A 202 CA CA A1264 1555 1555 2.46
LINK OE2 GLU A 205 CA CA A1264 1555 1555 2.52
LINK NE2 HIS A 222 ZN ZN A1261 1555 1555 2.18
LINK NE2 HIS A 226 ZN ZN A1261 1555 1555 2.19
LINK NE2 HIS A 232 ZN ZN A1261 1555 1555 2.10
LINK ZN ZN A1261 O HOH A2016 1555 1555 2.63
LINK ZN ZN A1261 O HOH A2023 1555 1555 2.25
LINK CA CA A1265 O HOH A2104 1555 1555 2.70
LINK CA CA A1265 O HOH A2116 1555 1555 2.90
LINK O ASP B 162 CA CA B1265 1555 1555 2.58
LINK NE2 HIS B 172 ZN ZN B1262 1555 1555 2.14
LINK OD2 ASP B 174 ZN ZN B1262 1555 1555 2.08
LINK OD1 ASP B 179 CA CA B1264 1555 1555 2.56
LINK O GLY B 180 CA CA B1264 1555 1555 2.47
LINK O SER B 182 CA CA B1264 1555 1555 2.61
LINK O LEU B 184 CA CA B1264 1555 1555 2.42
LINK NE2 HIS B 187 ZN ZN B1262 1555 1555 2.16
LINK O ASN B 194 CA CA B1265 1555 1555 2.61
LINK O GLY B 196 CA CA B1265 1555 1555 2.62
LINK OD1 ASP B 198 CA CA B1265 1555 1555 2.61
LINK ND1 HIS B 200 ZN ZN B1262 1555 1555 2.16
LINK OD2 ASP B 202 CA CA B1264 1555 1555 2.50
LINK OE2 GLU B 205 CA CA B1264 1555 1555 2.68
LINK NE2 HIS B 222 ZN ZN B1261 1555 1555 2.16
LINK NE2 HIS B 226 ZN ZN B1261 1555 1555 2.26
LINK NE2 HIS B 232 ZN ZN B1261 1555 1555 2.18
LINK ZN ZN B1261 O HOH B3012 1555 1555 2.62
LINK ZN ZN B1261 O HOH B3017 1555 1555 2.23
LINK CA CA B1265 O HOH B3077 1555 1555 2.75
LINK CA CA B1265 O HOH B3137 1555 1555 2.80
SITE 1 AC1 5 HIS A 222 HIS A 226 HIS A 232 HOH A2016
SITE 2 AC1 5 HOH A2023
SITE 1 AC2 4 HIS A 172 ASP A 174 HIS A 187 HIS A 200
SITE 1 AC3 6 ASP A 179 GLY A 180 SER A 182 LEU A 184
SITE 2 AC3 6 ASP A 202 GLU A 205
SITE 1 AC4 6 ASP A 162 ASN A 194 GLY A 196 ASP A 198
SITE 2 AC4 6 HOH A2104 HOH A2116
SITE 1 AC5 5 HIS B 222 HIS B 226 HIS B 232 HOH B3012
SITE 2 AC5 5 HOH B3017
SITE 1 AC6 4 HIS B 172 ASP B 174 HIS B 187 HIS B 200
SITE 1 AC7 6 ASP B 179 GLY B 180 SER B 182 LEU B 184
SITE 2 AC7 6 ASP B 202 GLU B 205
SITE 1 AC8 6 ASP B 162 ASN B 194 GLY B 196 ASP B 198
SITE 2 AC8 6 HOH B3077 HOH B3137
SITE 1 AC9 17 PHE A 217 LEU A 218 HIS A 222 ALA A 238
SITE 2 AC9 17 LEU A 239 PHE A 241 ILE A 243 TYR A 244
SITE 3 AC9 17 THR A 245 TYR A 246 THR A 247 LYS A 249
SITE 4 AC9 17 SER A 250 PHE A 252 HOH A2005 HOH A2009
SITE 5 AC9 17 HOH A2018
SITE 1 BC1 17 PHE B 217 LEU B 218 HIS B 222 ALA B 238
SITE 2 BC1 17 LEU B 239 PHE B 241 ILE B 243 TYR B 244
SITE 3 BC1 17 THR B 245 TYR B 246 THR B 247 LYS B 249
SITE 4 BC1 17 HIS B 251 PHE B 252 HOH B3004 HOH B3007
SITE 5 BC1 17 HOH B3014
CRYST1 134.508 36.486 95.586 90.00 130.52 90.00 C 1 2 1 8
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 0.007435 0.000000 0.006355 0.00000
SCALE2 0.000000 0.027408 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013763 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
