10 20 30 40 50 60 70 80 2OY2 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 21-FEB-07 2OY2
TITLE HUMAN MMP-8 IN COMPLEX WITH PEPTIDE IAG
COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUTROPHIL COLLAGENASE; COMPND 3 CHAIN: A, F; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: MATRIX METALLOPROTEINASE-8, MMP-8, PMNL COMPND 6 COLLAGENASE, PMNL-CL; COMPND 7 EC: 3.4.24.34; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: ILE-ALA-GLY PEPTIDE; COMPND 11 CHAIN: W, Y; COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MMP8, CLG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES
KEYWDS MMP-8, MATRIX METALLOPROTEINASE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR V.CALDERONE,I.BERTINI,M.FRAGAI,C.LUCHINAT,M.MALETTA,K.J.YEO
REVDAT 2 24-FEB-09 2OY2 1 VERSN REVDAT 1 06-MAR-07 2OY2 0
JRNL AUTH I.BERTINI,V.CALDERONE,M.FRAGAI,C.LUCHINAT, JRNL AUTH 2 M.MALETTA,K.J.YEO JRNL TITL SNAPSHOTS OF THE REACTION MECHANISM OF MATRIX JRNL TITL 2 METALLOPROTEINASES. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 45 7952 2006 JRNL REFN ISSN 1433-7851 JRNL PMID 17096442 JRNL DOI 10.1002/ANIE.200603100
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.MATTER,W.SCHWAB,D.BARBIER,G.BILLEN,B.HAASE, REMARK 1 AUTH 2 B.NEISES,M.SCHUDOK,W.THORWART,H.SCHREUDER, REMARK 1 AUTH 3 V.BRACHVOGEL REMARK 1 TITL CRYSTAL STRUCTURE OF MMP8 COMPLEXED WITH HMR2909 REMARK 1 REF J.MED.CHEM. V. 42 1908 1999 REMARK 1 REFN ISSN 0022-2623
REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 50507 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.200 REMARK 3 FREE R VALUE TEST SET COUNT : 5098 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3692 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.1560 REMARK 3 BIN FREE R VALUE SET COUNT : 374 REMARK 3 BIN FREE R VALUE : 0.2130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2516 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 565 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : -0.35000 REMARK 3 B33 (A**2) : 0.48000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.05000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.094 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.074 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.312 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2588 ; 0.008 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3524 ; 1.119 ; 1.921 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 316 ; 5.785 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 142 ;36.625 ;24.366 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 362 ;12.546 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;16.734 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 360 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2096 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1175 ; 0.193 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1816 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 371 ; 0.128 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 30 ; 0.088 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 57 ; 0.255 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 65 ; 0.115 ; 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): 1613 ; 0.762 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2530 ; 1.275 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1108 ; 2.291 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 994 ; 2.815 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2721 ; 2.179 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 575 ; 2.587 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2516 ; 1.716 ; 3.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 2OY2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-FEB-07. REMARK 100 THE RCSB ID CODE IS RCSB041726.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.84230 REMARK 200 MONOCHROMATOR : FIXED EXIT DOUBLE CRYSTAL SI REMARK 200 [111], HORIZONTALLY FOCUSSING REMARK 200 OPTICS : FIXED EXIT DOUBLE CRYSTAL SI REMARK 200 [111], HORIZONTALLY FOCUSSING REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55607 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 38.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : 0.08200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.31400 REMARK 200 R SYM FOR SHELL (I) : 0.31400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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: PDB ENTRY 1BZS REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, 20% PEG3350, 200MM REMARK 280 ACETOHYDROXAMIC ACID, 0.2M MGCL2, PH 8.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K
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 34.26650 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 300 REMARK: THE PROTEIN IS MONOMERIC IN VIVO BUT THERE ARE TWO REMARK 300 MOLECULES IN THE ASYMMETRIC UNIT.
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: 800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, W 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, Y 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 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 ASN A 85 REMARK 465 ASN F 85
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OXT GLY W 209 O HOH W 585 2.16 REMARK 500 OH TYR A 100 OE2 GLU A 110 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 111 CB - CA - C ANGL. DEV. = -12.9 DEGREES 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 ARG A 145 -131.54 47.07 REMARK 500 HIS A 147 29.09 -140.26 REMARK 500 ASN A 157 -161.15 68.32 REMARK 500 ARG F 145 -129.08 42.50 REMARK 500 HIS F 147 30.35 -141.21 REMARK 500 ASN F 157 -161.17 63.85 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 A1153 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH F1243 DISTANCE = 5.39 ANGSTROMS REMARK 525 HOH F1261 DISTANCE = 7.07 ANGSTROMS REMARK 525 HOH A1267 DISTANCE = 7.18 ANGSTROMS REMARK 525 HOH A1269 DISTANCE = 6.69 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 996 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 137 O REMARK 620 2 GLY A 169 O 163.5 REMARK 620 3 GLY A 171 O 95.3 96.7 REMARK 620 4 ASP A 173 OD1 88.7 102.9 88.7 REMARK 620 5 HOH A1027 O 83.1 87.3 82.5 167.3 REMARK 620 6 HOH A1015 O 84.4 82.3 172.9 98.4 90.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 998 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 147 NE2 REMARK 620 2 ASP A 149 OD2 106.7 REMARK 620 3 HIS A 162 NE2 114.0 117.1 REMARK 620 4 HIS A 175 ND1 107.5 95.6 114.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 997 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 154 OD1 REMARK 620 2 GLY A 155 O 89.5 REMARK 620 3 ASN A 157 O 86.9 86.3 REMARK 620 4 ILE A 159 O 87.3 176.8 93.5 REMARK 620 5 ASP A 177 OD2 95.0 84.7 170.8 95.6 REMARK 620 6 GLU A 180 OE2 172.8 93.6 86.8 89.6 91.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 999 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 197 NE2 REMARK 620 2 HIS A 201 NE2 103.2 REMARK 620 3 HIS A 207 NE2 105.9 100.6 REMARK 620 4 HOH A1183 O 118.3 134.9 85.2 REMARK 620 5 HOH A1059 O 98.5 95.9 146.4 62.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA F 996 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP F 137 O REMARK 620 2 GLY F 169 O 163.4 REMARK 620 3 GLY F 171 O 95.6 95.9 REMARK 620 4 ASP F 173 OD1 88.9 103.0 90.2 REMARK 620 5 HOH F1027 O 84.1 86.2 80.1 167.4 REMARK 620 6 HOH F1010 O 84.6 82.2 171.4 98.4 91.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN F 998 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS F 147 NE2 REMARK 620 2 ASP F 149 OD2 105.7 REMARK 620 3 HIS F 162 NE2 116.5 116.5 REMARK 620 4 HIS F 175 ND1 108.0 96.0 112.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA F 997 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP F 154 OD1 REMARK 620 2 GLY F 155 O 90.9 REMARK 620 3 ASN F 157 O 90.7 85.8 REMARK 620 4 ILE F 159 O 86.6 177.3 93.3 REMARK 620 5 ASP F 177 OD2 90.1 86.3 172.0 94.6 REMARK 620 6 GLU F 180 OE2 175.0 93.4 87.2 89.1 92.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN F 999 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS F 197 NE2 REMARK 620 2 HIS F 201 NE2 102.3 REMARK 620 3 HIS F 207 NE2 107.0 100.2 REMARK 620 4 HOH Y 59 O 100.9 95.4 144.0 REMARK 620 5 HOH Y 401 O 120.5 133.6 84.6 61.6 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 CA A 996 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 997 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 998 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 999 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA F 996 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA F 997 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN F 998 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN F 999
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BZS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MMP8 COMPLEXED WITH HMR2909 REMARK 900 RELATED ID: 2OY4 RELATED DB: PDB REMARK 900 RELATED ID: 2OXU RELATED DB: PDB REMARK 900 RELATED ID: 2OXW RELATED DB: PDB REMARK 900 RELATED ID: 2OXZ RELATED DB: PDB
DBREF 2OY2 A 85 242 UNP P22894 MMP8_HUMAN 105 262 DBREF 2OY2 F 85 242 UNP P22894 MMP8_HUMAN 105 262 DBREF 2OY2 W 207 209 PDB 2OY2 2OY2 207 209 DBREF 2OY2 Y 207 209 PDB 2OY2 2OY2 207 209
SEQRES 1 A 158 ASN PRO LYS TRP GLU ARG THR ASN LEU THR TYR ARG ILE SEQRES 2 A 158 ARG ASN TYR THR PRO GLN LEU SER GLU ALA GLU VAL GLU SEQRES 3 A 158 ARG ALA ILE LYS ASP ALA PHE GLU LEU TRP SER VAL ALA SEQRES 4 A 158 SER PRO LEU ILE PHE THR ARG ILE SER GLN GLY GLU ALA SEQRES 5 A 158 ASP ILE ASN ILE ALA PHE TYR GLN ARG ASP HIS GLY ASP SEQRES 6 A 158 ASN SER PRO PHE ASP GLY PRO ASN GLY ILE LEU ALA HIS SEQRES 7 A 158 ALA PHE GLN PRO GLY GLN GLY ILE GLY GLY ASP ALA HIS SEQRES 8 A 158 PHE ASP ALA GLU GLU THR TRP THR ASN THR SER ALA ASN SEQRES 9 A 158 TYR ASN LEU PHE LEU VAL ALA ALA HIS GLU PHE GLY HIS SEQRES 10 A 158 SER LEU GLY LEU ALA HIS SER SER ASP PRO GLY ALA LEU SEQRES 11 A 158 MET TYR PRO ASN TYR ALA PHE ARG GLU THR SER ASN TYR SEQRES 12 A 158 SER LEU PRO GLN ASP ASP ILE ASP GLY ILE GLN ALA ILE SEQRES 13 A 158 TYR GLY SEQRES 1 W 3 ILE ALA GLY SEQRES 1 F 158 ASN PRO LYS TRP GLU ARG THR ASN LEU THR TYR ARG ILE SEQRES 2 F 158 ARG ASN TYR THR PRO GLN LEU SER GLU ALA GLU VAL GLU SEQRES 3 F 158 ARG ALA ILE LYS ASP ALA PHE GLU LEU TRP SER VAL ALA SEQRES 4 F 158 SER PRO LEU ILE PHE THR ARG ILE SER GLN GLY GLU ALA SEQRES 5 F 158 ASP ILE ASN ILE ALA PHE TYR GLN ARG ASP HIS GLY ASP SEQRES 6 F 158 ASN SER PRO PHE ASP GLY PRO ASN GLY ILE LEU ALA HIS SEQRES 7 F 158 ALA PHE GLN PRO GLY GLN GLY ILE GLY GLY ASP ALA HIS SEQRES 8 F 158 PHE ASP ALA GLU GLU THR TRP THR ASN THR SER ALA ASN SEQRES 9 F 158 TYR ASN LEU PHE LEU VAL ALA ALA HIS GLU PHE GLY HIS SEQRES 10 F 158 SER LEU GLY LEU ALA HIS SER SER ASP PRO GLY ALA LEU SEQRES 11 F 158 MET TYR PRO ASN TYR ALA PHE ARG GLU THR SER ASN TYR SEQRES 12 F 158 SER LEU PRO GLN ASP ASP ILE ASP GLY ILE GLN ALA ILE SEQRES 13 F 158 TYR GLY SEQRES 1 Y 3 ILE ALA GLY
HET CA A 996 1 HET CA A 997 1 HET ZN A 998 1 HET ZN A 999 1 HET CA F 996 1 HET CA F 997 1 HET ZN F 998 1 HET ZN F 999 1
HETNAM CA CALCIUM ION HETNAM ZN ZINC ION
FORMUL 5 CA 4(CA 2+) FORMUL 7 ZN 4(ZN 2+) FORMUL 13 HOH *565(H2 O)
HELIX 1 1 SER A 105 VAL A 122 1 18 HELIX 2 2 ASN A 190 LEU A 203 1 14 HELIX 3 3 PRO A 230 TYR A 241 1 12 HELIX 4 4 SER F 105 VAL F 122 1 18 HELIX 5 5 ASN F 190 GLY F 204 1 15 HELIX 6 6 PRO F 230 GLY F 242 1 13
SHEET 1 A 5 ILE A 127 ARG A 130 0 SHEET 2 A 5 ASN A 92 ILE A 97 1 N LEU A 93 O THR A 129 SHEET 3 A 5 ILE A 138 TYR A 143 1 O ILE A 138 N THR A 94 SHEET 4 A 5 ALA A 174 ASP A 177 1 O ALA A 174 N ASN A 139 SHEET 5 A 5 ALA A 161 ALA A 163 -1 N HIS A 162 O HIS A 175 SHEET 1 B 5 ILE F 127 ARG F 130 0 SHEET 2 B 5 ASN F 92 ILE F 97 1 N LEU F 93 O THR F 129 SHEET 3 B 5 ILE F 138 TYR F 143 1 O ILE F 140 N ARG F 96 SHEET 4 B 5 ALA F 174 ASP F 177 1 O ALA F 174 N ASN F 139 SHEET 5 B 5 ALA F 161 ALA F 163 -1 N HIS F 162 O HIS F 175
LINK O ASP A 137 CA CA A 996 1555 1555 2.35 LINK NE2 HIS A 147 ZN ZN A 998 1555 1555 2.03 LINK OD2 ASP A 149 ZN ZN A 998 1555 1555 1.91 LINK OD1 ASP A 154 CA CA A 997 1555 1555 2.35 LINK O GLY A 155 CA CA A 997 1555 1555 2.28 LINK O ASN A 157 CA CA A 997 1555 1555 2.33 LINK O ILE A 159 CA CA A 997 1555 1555 2.31 LINK NE2 HIS A 162 ZN ZN A 998 1555 1555 2.05 LINK O GLY A 169 CA CA A 996 1555 1555 2.30 LINK O GLY A 171 CA CA A 996 1555 1555 2.32 LINK OD1 ASP A 173 CA CA A 996 1555 1555 2.45 LINK ND1 HIS A 175 ZN ZN A 998 1555 1555 2.09 LINK OD2 ASP A 177 CA CA A 997 1555 1555 2.35 LINK OE2 GLU A 180 CA CA A 997 1555 1555 2.30 LINK NE2 HIS A 197 ZN ZN A 999 1555 1555 2.07 LINK NE2 HIS A 201 ZN ZN A 999 1555 1555 2.10 LINK NE2 HIS A 207 ZN ZN A 999 1555 1555 2.04 LINK O ASP F 137 CA CA F 996 1555 1555 2.34 LINK NE2 HIS F 147 ZN ZN F 998 1555 1555 2.04 LINK OD2 ASP F 149 ZN ZN F 998 1555 1555 1.95 LINK OD1 ASP F 154 CA CA F 997 1555 1555 2.37 LINK O GLY F 155 CA CA F 997 1555 1555 2.24 LINK O ASN F 157 CA CA F 997 1555 1555 2.32 LINK O ILE F 159 CA CA F 997 1555 1555 2.32 LINK NE2 HIS F 162 ZN ZN F 998 1555 1555 2.02 LINK O GLY F 169 CA CA F 996 1555 1555 2.31 LINK O GLY F 171 CA CA F 996 1555 1555 2.32 LINK OD1 ASP F 173 CA CA F 996 1555 1555 2.47 LINK ND1 HIS F 175 ZN ZN F 998 1555 1555 2.06 LINK OD2 ASP F 177 CA CA F 997 1555 1555 2.37 LINK OE2 GLU F 180 CA CA F 997 1555 1555 2.31 LINK NE2 HIS F 197 ZN ZN F 999 1555 1555 2.06 LINK NE2 HIS F 201 ZN ZN F 999 1555 1555 2.12 LINK NE2 HIS F 207 ZN ZN F 999 1555 1555 2.00 LINK CA CA A 996 O HOH A1027 1555 1555 2.46 LINK CA CA A 996 O HOH A1015 1555 1555 2.32 LINK ZN ZN A 999 O HOH A1183 1555 1555 2.35 LINK ZN ZN A 999 O HOH A1059 1555 1555 2.27 LINK CA CA F 996 O HOH F1027 1555 1555 2.42 LINK CA CA F 996 O HOH F1010 1555 1555 2.35 LINK ZN ZN F 999 O HOH Y 59 1555 1555 2.19 LINK ZN ZN F 999 O HOH Y 401 1555 1555 2.48
CISPEP 1 ASN A 188 TYR A 189 0 -5.05 CISPEP 2 ASN F 188 TYR F 189 0 -5.36
SITE 1 AC1 6 ASP A 137 GLY A 169 GLY A 171 ASP A 173 SITE 2 AC1 6 HOH A1015 HOH A1027 SITE 1 AC2 6 ASP A 154 GLY A 155 ASN A 157 ILE A 159 SITE 2 AC2 6 ASP A 177 GLU A 180 SITE 1 AC3 4 HIS A 147 ASP A 149 HIS A 162 HIS A 175 SITE 1 AC4 5 HIS A 197 HIS A 201 HIS A 207 HOH A1059 SITE 2 AC4 5 HOH A1183 SITE 1 AC5 6 ASP F 137 GLY F 169 GLY F 171 ASP F 173 SITE 2 AC5 6 HOH F1010 HOH F1027 SITE 1 AC6 6 ASP F 154 GLY F 155 ASN F 157 ILE F 159 SITE 2 AC6 6 ASP F 177 GLU F 180 SITE 1 AC7 4 HIS F 147 ASP F 149 HIS F 162 HIS F 175 SITE 1 AC8 5 HIS F 197 HIS F 201 HIS F 207 HOH Y 59 SITE 2 AC8 5 HOH Y 401
CRYST1 33.207 68.533 78.281 90.00 98.10 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 0.030114 0.000000 0.004288 0.00000
SCALE2 0.000000 0.014591 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012903 0.00000