HEADER HYDROLASE 19-MAR-13 4JPA
TITLE MMP13 IN COMPLEX WITH A PIPERAZINE HYDANTOIN LIGAND
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: COLLAGENASE 3;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: UNP RESIDUES 103-274;
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_TAXID: 9606;
SOURCE 4 GENE: MMP13;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS MATRIX METALLOPROTEASE, CALCIUM BINDING, ZINC BINDING, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.GERHARDT,D.HARGREAVES
REVDAT 3 20-MAR-24 4JPA 1 REMARK SEQADV LINK
REVDAT 2 15-NOV-17 4JPA 1 REMARK
REVDAT 1 05-MAR-14 4JPA 0
JRNL AUTH C.DE SAVI,D.WATERSON,A.PAPE,S.LAMONT,E.HADLEY,M.MILLS,
JRNL AUTH 2 K.M.PAGE,J.BOWYER,R.A.MACIEWICZ
JRNL TITL HYDANTOIN BASED INHIBITORS OF MMP13--DISCOVERY OF AZD6605.
JRNL REF BIOORG.MED.CHEM.LETT. V. 23 4705 2013
JRNL REFN ISSN 0960-894X
JRNL PMID 23810497
JRNL DOI 10.1016/J.BMCL.2013.05.089
REMARK 2
REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0005
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.90
REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9
REMARK 3 NUMBER OF REFLECTIONS : 21114
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.180
REMARK 3 R VALUE (WORKING SET) : 0.177
REMARK 3 FREE R VALUE : 0.230
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 1140
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1475
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.74
REMARK 3 BIN R VALUE (WORKING SET) : 0.2170
REMARK 3 BIN FREE R VALUE SET COUNT : 64
REMARK 3 BIN FREE R VALUE : 0.3200
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2641
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 78
REMARK 3 SOLVENT ATOMS : 373
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.43
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.95000
REMARK 3 B22 (A**2) : 0.08000
REMARK 3 B33 (A**2) : -1.63000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -1.77000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.219
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.183
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.119
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.549
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2810 ; 0.007 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): 2297 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3827 ; 1.207 ; 1.966
REMARK 3 BOND ANGLES OTHERS (DEGREES): 5376 ; 0.717 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 328 ; 5.920 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;36.383 ;23.985
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 402 ;13.500 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;17.685 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 375 ; 0.062 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3184 ; 0.003 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 596 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 601 ; 0.196 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2243 ; 0.165 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1367 ; 0.196 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): 1388 ; 0.082 ; 0.200
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 245 ; 0.123 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 29 ; 0.119 ; 0.200
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 17 ; 0.163 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): 86 ; 0.195 ; 0.200
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 32 ; 0.120 ; 0.200
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1645 ; 0.381 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 673 ; 0.062 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2647 ; 0.713 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1217 ; 0.952 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1180 ; 1.427 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 8
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 104 A 272
REMARK 3 RESIDUE RANGE : B 104 B 269
REMARK 3 RESIDUE RANGE : A 301 A 305
REMARK 3 RESIDUE RANGE : B 301 B 305
REMARK 3 RESIDUE RANGE : A 306 A 306
REMARK 3 RESIDUE RANGE : B 306 B 306
REMARK 3 RESIDUE RANGE : A 401 A 589
REMARK 3 RESIDUE RANGE : B 401 B 584
REMARK 3 ORIGIN FOR THE GROUP (A): 26.0860 0.1641 20.7925
REMARK 3 T TENSOR
REMARK 3 T11: -0.0180 T22: -0.0333
REMARK 3 T33: -0.0018 T12: -0.0036
REMARK 3 T13: -0.0018 T23: 0.0018
REMARK 3 L TENSOR
REMARK 3 L11: 0.2552 L22: 0.0910
REMARK 3 L33: 0.2516 L12: -0.0489
REMARK 3 L13: -0.0101 L23: 0.0154
REMARK 3 S TENSOR
REMARK 3 S11: 0.0140 S12: 0.0088 S13: -0.0003
REMARK 3 S21: -0.0157 S22: -0.0082 S23: 0.0140
REMARK 3 S31: -0.0116 S32: 0.0103 S33: -0.0058
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : BABINET MODEL WITH MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 4JPA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-DEC-13.
REMARK 100 THE DEPOSITION ID IS D_1000078332.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 20-OCT-06
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E DW
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALA, SCALEPACK, D*TREK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23627
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000
REMARK 200 RESOLUTION RANGE LOW (A) : 35.900
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.600
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.89
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 27.5% PEG 4000 1.25M AMFORMATE, 100MM
REMARK 280 TRISHCL PH 8.5 , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K
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 67.38550
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.99300
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.38550
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.99300
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
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: 2860 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 16190 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH B 436 LIES ON A SPECIAL POSITION.
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 MET A 102
REMARK 465 GLU A 103
REMARK 465 THR A 247
REMARK 465 GLY A 248
REMARK 465 LYS A 249
REMARK 465 SER A 250
REMARK 465 PRO A 273
REMARK 465 ASN A 274
REMARK 465 MET B 102
REMARK 465 GLU B 103
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: 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 -129.88 44.34
REMARK 500 SER A 182 -166.03 58.02
REMARK 500 ASN A 194 -114.00 57.81
REMARK 500 SER A 210 -160.36 -123.84
REMARK 500 ASP A 231 -156.02 -96.03
REMARK 500 PRO A 242 49.15 -78.62
REMARK 500 LYS B 170 -131.88 47.39
REMARK 500 TYR B 176 70.40 -111.24
REMARK 500 SER B 182 -172.34 68.61
REMARK 500 ASN B 194 -119.57 59.14
REMARK 500 SER B 210 -117.19 -119.10
REMARK 500 PRO B 242 47.74 -78.33
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 NA A 305 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 128 OD2
REMARK 620 2 ASP A 203 O 162.4
REMARK 620 3 ASP A 203 OD2 94.1 70.9
REMARK 620 4 GLU A 205 O 81.7 94.2 108.7
REMARK 620 5 HOH A 526 O 115.5 78.5 106.4 139.4
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 302 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 162 O
REMARK 620 2 ASN A 194 O 174.5
REMARK 620 3 GLY A 196 O 90.9 94.6
REMARK 620 4 ASP A 198 OD1 83.8 97.0 91.6
REMARK 620 5 HOH A 402 O 91.8 88.1 81.1 171.4
REMARK 620 6 HOH A 584 O 93.1 81.4 171.1 96.7 90.9
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 303 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 172 NE2
REMARK 620 2 ASP A 174 OD2 114.2
REMARK 620 3 HIS A 187 NE2 116.7 113.3
REMARK 620 4 HIS A 200 ND1 110.6 91.5 107.6
REMARK 620 N 1 2 3
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 179 OD1
REMARK 620 2 GLY A 180 O 92.0
REMARK 620 3 SER A 182 O 86.9 90.0
REMARK 620 4 LEU A 184 O 85.0 172.6 96.5
REMARK 620 5 ASP A 202 OD2 91.6 86.2 175.9 87.1
REMARK 620 6 GLU A 205 OE2 169.5 97.3 88.3 86.3 93.8
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 222 NE2
REMARK 620 2 HIS A 226 NE2 100.4
REMARK 620 3 HIS A 232 NE2 112.7 101.5
REMARK 620 4 AZ6 A 306 N7 113.6 124.3 104.0
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA B 305 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 128 OD2
REMARK 620 2 ASP B 203 OD2 99.8
REMARK 620 3 ASP B 203 O 166.3 71.4
REMARK 620 4 GLU B 205 O 83.2 110.1 90.0
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 162 O
REMARK 620 2 ASN B 194 O 173.5
REMARK 620 3 GLY B 196 O 91.4 94.6
REMARK 620 4 ASP B 198 OD1 85.5 96.5 92.0
REMARK 620 5 HOH B 427 O 87.7 91.7 75.1 165.3
REMARK 620 6 HOH B 428 O 89.4 84.2 166.6 101.4 91.6
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 172 NE2
REMARK 620 2 ASP B 174 OD2 112.6
REMARK 620 3 HIS B 187 NE2 113.5 116.9
REMARK 620 4 HIS B 200 ND1 104.7 90.0 116.4
REMARK 620 N 1 2 3
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 179 OD1
REMARK 620 2 GLY B 180 O 85.8
REMARK 620 3 SER B 182 O 86.3 85.5
REMARK 620 4 LEU B 184 O 90.3 175.6 96.4
REMARK 620 5 ASP B 202 OD2 93.4 86.9 172.4 91.2
REMARK 620 6 GLU B 205 OE2 173.9 92.8 87.6 91.2 92.5
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 222 NE2
REMARK 620 2 HIS B 226 NE2 97.4
REMARK 620 3 HIS B 232 NE2 107.5 105.1
REMARK 620 4 AZ6 B 306 N7 116.5 121.2 108.0
REMARK 620 N 1 2 3
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 CA A 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN 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 NA A 305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZ6 A 306
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 304
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 305
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZ6 B 306
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4JP4 RELATED DB: PDB
REMARK 900 MMP13 IN COMPLEX WITH AZD6605
DBREF 4JPA A 103 274 UNP P45452 MMP13_HUMAN 103 274
DBREF 4JPA B 103 274 UNP P45452 MMP13_HUMAN 103 274
SEQADV 4JPA MET A 102 UNP P45452 EXPRESSION TAG
SEQADV 4JPA MET B 102 UNP P45452 EXPRESSION TAG
SEQRES 1 A 173 MET GLU TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER
SEQRES 2 A 173 LYS MET ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO
SEQRES 3 A 173 ASP MET THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS
SEQRES 4 A 173 ALA PHE LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE
SEQRES 5 A 173 THR ARG LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER
SEQRES 6 A 173 PHE GLY ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP
SEQRES 7 A 173 GLY PRO SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY
SEQRES 8 A 173 PRO ASN TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU
SEQRES 9 A 173 THR TRP THR SER SER SER LYS GLY TYR ASN LEU PHE LEU
SEQRES 10 A 173 VAL ALA ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP
SEQRES 11 A 173 HIS SER LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR
SEQRES 12 A 173 THR TYR THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP
SEQRES 13 A 173 ASP VAL GLN GLY ILE GLN SER LEU TYR GLY PRO GLY ASP
SEQRES 14 A 173 GLU ASP PRO ASN
SEQRES 1 B 173 MET GLU TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER
SEQRES 2 B 173 LYS MET ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO
SEQRES 3 B 173 ASP MET THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS
SEQRES 4 B 173 ALA PHE LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE
SEQRES 5 B 173 THR ARG LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER
SEQRES 6 B 173 PHE GLY ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP
SEQRES 7 B 173 GLY PRO SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY
SEQRES 8 B 173 PRO ASN TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU
SEQRES 9 B 173 THR TRP THR SER SER SER LYS GLY TYR ASN LEU PHE LEU
SEQRES 10 B 173 VAL ALA ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP
SEQRES 11 B 173 HIS SER LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR
SEQRES 12 B 173 THR TYR THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP
SEQRES 13 B 173 ASP VAL GLN GLY ILE GLN SER LEU TYR GLY PRO GLY ASP
SEQRES 14 B 173 GLU ASP PRO ASN
HET ZN A 301 1
HET CA A 302 1
HET ZN A 303 1
HET CA A 304 1
HET NA A 305 1
HET AZ6 A 306 34
HET ZN B 301 1
HET ZN B 302 1
HET CA B 303 1
HET CA B 304 1
HET NA B 305 1
HET AZ6 B 306 34
HETNAM ZN ZINC ION
HETNAM CA CALCIUM ION
HETNAM NA SODIUM ION
HETNAM AZ6 3-[({2-[4-({[(4S)-4-METHYL-2,5-DIOXOIMIDAZOLIDIN-4-
HETNAM 2 AZ6 YL]METHYL}SULFONYL)PIPERAZIN-1-YL]PYRIMIDIN-5-YL}OXY)
HETNAM 3 AZ6 METHYL]BENZONITRILE
FORMUL 3 ZN 4(ZN 2+)
FORMUL 4 CA 4(CA 2+)
FORMUL 7 NA 2(NA 1+)
FORMUL 8 AZ6 2(C21 H23 N7 O5 S)
FORMUL 15 HOH *373(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 GLY B 229 1 14
HELIX 6 6 PRO B 255 GLY B 267 1 13
SHEET 1 A 5 ASN A 152 ARG A 155 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 LEU B 156 0
SHEET 2 C 5 ASN B 117 ILE B 122 1 N TYR B 120 O LEU B 156
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 SER B 166
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 OD2 ASP A 128 NA NA A 305 1555 1555 2.53
LINK O ASP A 162 CA CA A 302 1555 1555 2.42
LINK NE2 HIS A 172 ZN ZN A 303 1555 1555 2.06
LINK OD2 ASP A 174 ZN ZN A 303 1555 1555 1.96
LINK OD1 ASP A 179 CA CA A 304 1555 1555 2.46
LINK O GLY A 180 CA CA A 304 1555 1555 2.22
LINK O SER A 182 CA CA A 304 1555 1555 2.37
LINK O LEU A 184 CA CA A 304 1555 1555 2.34
LINK NE2 HIS A 187 ZN ZN A 303 1555 1555 2.04
LINK O ASN A 194 CA CA A 302 1555 1555 2.29
LINK O GLY A 196 CA CA A 302 1555 1555 2.31
LINK OD1 ASP A 198 CA CA A 302 1555 1555 2.47
LINK ND1 HIS A 200 ZN ZN A 303 1555 1555 2.08
LINK OD2 ASP A 202 CA CA A 304 1555 1555 2.22
LINK O ASP A 203 NA NA A 305 1555 1555 2.61
LINK OD2 ASP A 203 NA NA A 305 1555 1555 2.64
LINK OE2 GLU A 205 CA CA A 304 1555 1555 2.16
LINK O GLU A 205 NA NA A 305 1555 1555 2.44
LINK NE2 HIS A 222 ZN ZN A 301 1555 1555 2.10
LINK NE2 HIS A 226 ZN ZN A 301 1555 1555 2.08
LINK NE2 HIS A 232 ZN ZN A 301 1555 1555 2.07
LINK ZN ZN A 301 N7 AZ6 A 306 1555 1555 2.04
LINK CA CA A 302 O HOH A 402 1555 1555 2.32
LINK CA CA A 302 O HOH A 584 1555 1555 2.37
LINK NA NA A 305 O HOH A 526 1555 1555 2.65
LINK OD2 ASP B 128 NA NA B 305 1555 1555 2.34
LINK O ASP B 162 CA CA B 303 1555 1555 2.27
LINK NE2 HIS B 172 ZN ZN B 302 1555 1555 2.05
LINK OD2 ASP B 174 ZN ZN B 302 1555 1555 1.94
LINK OD1 ASP B 179 CA CA B 304 1555 1555 2.34
LINK O GLY B 180 CA CA B 304 1555 1555 2.35
LINK O SER B 182 CA CA B 304 1555 1555 2.36
LINK O LEU B 184 CA CA B 304 1555 1555 2.29
LINK NE2 HIS B 187 ZN ZN B 302 1555 1555 2.20
LINK O ASN B 194 CA CA B 303 1555 1555 2.28
LINK O GLY B 196 CA CA B 303 1555 1555 2.40
LINK OD1 ASP B 198 CA CA B 303 1555 1555 2.49
LINK ND1 HIS B 200 ZN ZN B 302 1555 1555 2.09
LINK OD2 ASP B 202 CA CA B 304 1555 1555 2.32
LINK OD2 ASP B 203 NA NA B 305 1555 1555 2.61
LINK O ASP B 203 NA NA B 305 1555 1555 2.68
LINK OE2 GLU B 205 CA CA B 304 1555 1555 2.19
LINK O GLU B 205 NA NA B 305 1555 1555 2.41
LINK NE2 HIS B 222 ZN ZN B 301 1555 1555 2.12
LINK NE2 HIS B 226 ZN ZN B 301 1555 1555 2.08
LINK NE2 HIS B 232 ZN ZN B 301 1555 1555 2.04
LINK ZN ZN B 301 N7 AZ6 B 306 1555 1555 2.05
LINK CA CA B 303 O HOH B 427 1555 1555 2.39
LINK CA CA B 303 O HOH B 428 1555 1555 2.18
SITE 1 AC1 4 HIS A 222 HIS A 226 HIS A 232 AZ6 A 306
SITE 1 AC2 6 ASP A 162 ASN A 194 GLY A 196 ASP A 198
SITE 2 AC2 6 HOH A 402 HOH A 584
SITE 1 AC3 4 HIS A 172 ASP A 174 HIS A 187 HIS A 200
SITE 1 AC4 6 ASP A 179 GLY A 180 SER A 182 LEU A 184
SITE 2 AC4 6 ASP A 202 GLU A 205
SITE 1 AC5 4 ASP A 128 ASP A 203 GLU A 205 HOH A 526
SITE 1 AC6 20 LEU A 184 LEU A 185 ALA A 186 HIS A 187
SITE 2 AC6 20 LEU A 218 HIS A 222 GLU A 223 HIS A 226
SITE 3 AC6 20 HIS A 232 GLY A 237 ALA A 238 LEU A 239
SITE 4 AC6 20 PHE A 241 PRO A 242 ILE A 243 TYR A 244
SITE 5 AC6 20 THR A 245 TYR A 246 ZN A 301 HOH A 445
SITE 1 AC7 4 HIS B 222 HIS B 226 HIS B 232 AZ6 B 306
SITE 1 AC8 4 HIS B 172 ASP B 174 HIS B 187 HIS B 200
SITE 1 AC9 6 ASP B 162 ASN B 194 GLY B 196 ASP B 198
SITE 2 AC9 6 HOH B 427 HOH B 428
SITE 1 BC1 6 ASP B 179 GLY B 180 SER B 182 LEU B 184
SITE 2 BC1 6 ASP B 202 GLU B 205
SITE 1 BC2 4 HOH A 529 ASP B 128 ASP B 203 GLU B 205
SITE 1 BC3 20 GLY B 183 LEU B 185 ALA B 186 LEU B 218
SITE 2 BC3 20 HIS B 222 GLU B 223 HIS B 226 HIS B 232
SITE 3 BC3 20 ALA B 238 LEU B 239 PHE B 241 ILE B 243
SITE 4 BC3 20 TYR B 244 THR B 245 TYR B 246 THR B 247
SITE 5 BC3 20 ZN B 301 HOH B 507 HOH B 513 HOH B 560
CRYST1 134.771 35.986 101.492 90.00 134.99 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 0.007420 0.000000 0.007417 0.00000
SCALE2 0.000000 0.027789 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013932 0.00000
(ATOM LINES ARE NOT SHOWN.)
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