HEADER HYDROLASE 24-JUL-23 8K5W TITLE CRYSTAL STRUCTURE OF HUMAN PROMMP-9 CATALYTIC DOMAIN IN COMPLEX WITH TITLE 2 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: MATRIX METALLOPROTEINASE-9; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MMP-9,92 KDA GELATINASE,92 KDA TYPE IV COLLAGENASE, COMPND 5 GELATINASE B,GELB; COMPND 6 EC: 3.4.24.35; 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 GENE: MMP9, CLG4B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MMP-9, 92 KDA GELATINASE, 92 KDA TYPE IV COLLAGENASE, GELATINASE B, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KAMITANI,M.MIMA,R.NISHIKAWA-SHIMONO REVDAT 1 06-DEC-23 8K5W 0 JRNL AUTH R.NISHIKAWA-SHIMONO,M.KUWABARA,S.FUJISAKI,D.MATSUDA,M.ENDO, JRNL AUTH 2 M.KAMITANI,A.FUTAMURA,Y.NOMURA,T.YAMAGUCHI-SASAKI, JRNL AUTH 3 T.YABUUCHI,C.YAMAGUCHI,N.TANAKA-YAMAMOTO,S.SATAKE, JRNL AUTH 4 K.ABE-SATO,K.FUNAYAMA,M.SAKATA,S.TAKAHASHI,K.HIRANO, JRNL AUTH 5 T.FUKUNAGA,Y.UOZUMI,S.KATO,Y.TAMURA,T.NAKAMORI,M.MIMA, JRNL AUTH 6 C.MISHIMA-TSUMAGARI,D.NOZAWA,Y.IMAI,T.ASAMI JRNL TITL DISCOVERY OF NOVEL INDOLE DERIVATIVES AS POTENT AND JRNL TITL 2 SELECTIVE INHIBITORS OF PROMMP-9 ACTIVATION. JRNL REF BIOORG.MED.CHEM.LETT. V. 97 29541 2023 JRNL REFN ESSN 1464-3405 JRNL PMID 37952596 JRNL DOI 10.1016/J.BMCL.2023.129541 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 21.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 30761 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) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1642 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) : 2256 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.37 REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE SET COUNT : 124 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3523 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 83 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.23000 REMARK 3 B22 (A**2) : -3.26000 REMARK 3 B33 (A**2) : 2.99000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.69000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.223 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.194 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.182 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.024 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3719 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3319 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5066 ; 1.588 ; 1.671 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7653 ; 1.325 ; 1.604 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 442 ; 7.362 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 204 ;32.114 ;21.912 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 538 ;15.341 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;23.410 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 439 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4249 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 883 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1777 ; 2.782 ; 3.692 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1775 ; 2.782 ; 3.691 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2213 ; 4.148 ; 5.513 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2213 ; 4.148 ; 5.513 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1942 ; 2.895 ; 3.997 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1939 ; 2.860 ; 3.995 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2847 ; 4.459 ; 5.880 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 17219 ; 7.896 ;69.495 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 17191 ; 7.894 ;69.487 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 8K5W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1300039625. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54056 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32566 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 21.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 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 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% W/V POLYETHYLENE GLYCOL 1500, REMARK 280 100MM SPG BUFFER PH5.0, VAPOR DIFFUSION, TEMPERATURE 293K 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 45.15950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.50100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.15950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.50100 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 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 28 REMARK 465 VAL A 29 REMARK 465 LEU A 30 REMARK 465 PHE A 31 REMARK 465 PRO A 32 REMARK 465 GLY A 33 REMARK 465 ASP A 34 REMARK 465 LEU A 35 REMARK 465 ARG A 36 REMARK 465 THR A 37 REMARK 465 ARG A 106 REMARK 465 PHE A 107 REMARK 465 GLN A 108 REMARK 465 MET B 28 REMARK 465 VAL B 29 REMARK 465 LEU B 30 REMARK 465 PHE B 31 REMARK 465 PRO B 32 REMARK 465 GLY B 33 REMARK 465 ASP B 34 REMARK 465 LEU B 35 REMARK 465 ARG B 36 REMARK 465 THR B 37 REMARK 465 ASN B 38 REMARK 465 LEU B 39 REMARK 465 ARG B 56 REMARK 465 VAL B 57 REMARK 465 ALA B 58 REMARK 465 GLU B 59 REMARK 465 MET B 60 REMARK 465 ARG B 61 REMARK 465 GLY B 62 REMARK 465 GLU B 63 REMARK 465 SER B 64 REMARK 465 LYS B 65 REMARK 465 SER B 66 REMARK 465 ARG B 106 REMARK 465 PHE B 107 REMARK 465 GLN B 108 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 A 467 O HOH A 467 2556 1.28 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 B 265 NE - CZ - NH2 ANGL. DEV. = 3.4 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 ALA A 173 -136.93 44.67 REMARK 500 TYR A 179 71.87 -119.04 REMARK 500 ASP A 185 -151.61 58.42 REMARK 500 PRO A 194 154.02 -47.86 REMARK 500 SER A 211 -159.87 -145.00 REMARK 500 LEU A 267 -52.95 -124.36 REMARK 500 ASP B 163 82.19 -69.38 REMARK 500 ALA B 173 -133.07 48.11 REMARK 500 TYR B 179 74.76 -117.00 REMARK 500 ASP B 185 -159.56 53.78 REMARK 500 LYS B 214 94.27 -69.66 REMARK 500 GLN B 216 95.32 -58.71 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 99 SG REMARK 620 2 HIS A 226 NE2 113.3 REMARK 620 3 HIS A 230 NE2 118.3 97.9 REMARK 620 4 HIS A 236 NE2 115.3 108.3 101.7 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 131 OD2 REMARK 620 2 ASP A 206 O 170.9 REMARK 620 3 ASP A 206 OD1 96.3 80.9 REMARK 620 4 GLU A 208 O 84.2 89.3 116.3 REMARK 620 N 1 2 3 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 171.8 REMARK 620 3 GLN A 199 O 107.0 81.2 REMARK 620 4 ASP A 201 OD1 88.0 91.3 96.9 REMARK 620 N 1 2 3 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 OD2 108.5 REMARK 620 3 HIS A 190 NE2 108.6 114.8 REMARK 620 4 HIS A 203 ND1 116.3 91.8 115.9 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 82.1 REMARK 620 3 ASP A 185 O 88.8 93.3 REMARK 620 4 LEU A 187 O 93.8 172.2 93.2 REMARK 620 5 ASP A 205 OD2 95.4 82.4 173.6 91.4 REMARK 620 6 GLU A 208 OE2 169.5 95.6 81.1 89.6 94.5 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 CYS B 99 SG REMARK 620 2 HIS B 226 NE2 112.9 REMARK 620 3 HIS B 230 NE2 114.6 104.2 REMARK 620 4 HIS B 236 NE2 127.5 98.5 95.6 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 131 OD2 REMARK 620 2 ASP B 206 O 160.5 REMARK 620 3 ASP B 206 OD1 92.7 70.7 REMARK 620 4 GLU B 208 O 88.0 88.1 110.0 REMARK 620 N 1 2 3 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 163.9 REMARK 620 3 GLN B 199 O 105.9 89.0 REMARK 620 4 ASP B 201 OD1 90.0 95.5 93.3 REMARK 620 5 HOH B 413 O 87.9 88.8 79.4 171.4 REMARK 620 6 HOH B 430 O 81.6 83.0 171.1 91.5 96.3 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 OD2 107.9 REMARK 620 3 HIS B 190 NE2 111.9 117.1 REMARK 620 4 HIS B 203 ND1 99.2 93.8 124.2 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 91.1 REMARK 620 3 ASP B 185 O 97.5 87.6 REMARK 620 4 LEU B 187 O 90.7 175.8 95.9 REMARK 620 5 ASP B 205 OD2 93.4 80.5 164.1 95.6 REMARK 620 6 GLU B 208 OE2 175.7 89.1 78.2 89.4 90.9 REMARK 620 N 1 2 3 4 5 DBREF 8K5W A 29 215 UNP P14780 MMP9_HUMAN 29 215 DBREF 8K5W A 216 269 UNP P14780 MMP9_HUMAN 391 444 DBREF 8K5W B 29 215 UNP P14780 MMP9_HUMAN 29 215 DBREF 8K5W B 216 269 UNP P14780 MMP9_HUMAN 391 444 SEQADV 8K5W MET A 28 UNP P14780 INITIATING METHIONINE SEQADV 8K5W MET B 28 UNP P14780 INITIATING METHIONINE SEQRES 1 A 242 MET VAL LEU PHE PRO GLY ASP LEU ARG THR ASN LEU THR SEQRES 2 A 242 ASP ARG GLN LEU ALA GLU GLU TYR LEU TYR ARG TYR GLY SEQRES 3 A 242 TYR THR ARG VAL ALA GLU MET ARG GLY GLU SER LYS SER SEQRES 4 A 242 LEU GLY PRO ALA LEU LEU LEU LEU GLN LYS GLN LEU SER SEQRES 5 A 242 LEU PRO GLU THR GLY GLU LEU ASP SER ALA THR LEU LYS SEQRES 6 A 242 ALA MET ARG THR PRO ARG CYS GLY VAL PRO ASP LEU GLY SEQRES 7 A 242 ARG PHE GLN THR PHE GLU GLY ASP LEU LYS TRP HIS HIS SEQRES 8 A 242 HIS ASN ILE THR TYR TRP ILE GLN ASN TYR SER GLU ASP SEQRES 9 A 242 LEU PRO ARG ALA VAL ILE ASP ASP ALA PHE ALA ARG ALA SEQRES 10 A 242 PHE ALA LEU TRP SER ALA VAL THR PRO LEU THR PHE THR SEQRES 11 A 242 ARG VAL TYR SER ARG ASP ALA ASP ILE VAL ILE GLN PHE SEQRES 12 A 242 GLY VAL ALA GLU HIS GLY ASP GLY TYR PRO PHE ASP GLY SEQRES 13 A 242 LYS ASP GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO SEQRES 14 A 242 GLY ILE GLN GLY ASP ALA HIS PHE ASP ASP ASP GLU LEU SEQRES 15 A 242 TRP SER LEU GLY LYS GLY GLN GLY TYR SER LEU PHE LEU SEQRES 16 A 242 VAL ALA ALA HIS GLU PHE GLY HIS ALA LEU GLY LEU ASP SEQRES 17 A 242 HIS SER SER VAL PRO GLU ALA LEU MET TYR PRO MET TYR SEQRES 18 A 242 ARG PHE THR GLU GLY PRO PRO LEU HIS LYS ASP ASP VAL SEQRES 19 A 242 ASN GLY ILE ARG HIS LEU TYR GLY SEQRES 1 B 242 MET VAL LEU PHE PRO GLY ASP LEU ARG THR ASN LEU THR SEQRES 2 B 242 ASP ARG GLN LEU ALA GLU GLU TYR LEU TYR ARG TYR GLY SEQRES 3 B 242 TYR THR ARG VAL ALA GLU MET ARG GLY GLU SER LYS SER SEQRES 4 B 242 LEU GLY PRO ALA LEU LEU LEU LEU GLN LYS GLN LEU SER SEQRES 5 B 242 LEU PRO GLU THR GLY GLU LEU ASP SER ALA THR LEU LYS SEQRES 6 B 242 ALA MET ARG THR PRO ARG CYS GLY VAL PRO ASP LEU GLY SEQRES 7 B 242 ARG PHE GLN THR PHE GLU GLY ASP LEU LYS TRP HIS HIS SEQRES 8 B 242 HIS ASN ILE THR TYR TRP ILE GLN ASN TYR SER GLU ASP SEQRES 9 B 242 LEU PRO ARG ALA VAL ILE ASP ASP ALA PHE ALA ARG ALA SEQRES 10 B 242 PHE ALA LEU TRP SER ALA VAL THR PRO LEU THR PHE THR SEQRES 11 B 242 ARG VAL TYR SER ARG ASP ALA ASP ILE VAL ILE GLN PHE SEQRES 12 B 242 GLY VAL ALA GLU HIS GLY ASP GLY TYR PRO PHE ASP GLY SEQRES 13 B 242 LYS ASP GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO SEQRES 14 B 242 GLY ILE GLN GLY ASP ALA HIS PHE ASP ASP ASP GLU LEU SEQRES 15 B 242 TRP SER LEU GLY LYS GLY GLN GLY TYR SER LEU PHE LEU SEQRES 16 B 242 VAL ALA ALA HIS GLU PHE GLY HIS ALA LEU GLY LEU ASP SEQRES 17 B 242 HIS SER SER VAL PRO GLU ALA LEU MET TYR PRO MET TYR SEQRES 18 B 242 ARG PHE THR GLU GLY PRO PRO LEU HIS LYS ASP ASP VAL SEQRES 19 B 242 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 VOO A 306 34 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 VOO B 306 34 HET 2HP B 307 5 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM VOO 2-[[5-FLUORANYL-7-(METHYLAMINO)-1H-INDOL-2- HETNAM 2 VOO YL]CARBONYL]-N-(2-PYRROL-1-YLETHYL)-3,4-DIHYDRO-1H- HETNAM 3 VOO ISOQUINOLINE-7-CARBOXAMIDE HETNAM 2HP DIHYDROGENPHOSPHATE ION FORMUL 3 ZN 4(ZN 2+) FORMUL 5 CA 6(CA 2+) FORMUL 8 VOO 2(C26 H26 F N5 O2) FORMUL 15 2HP H2 O4 P 1- FORMUL 16 HOH *128(H2 O) HELIX 1 AA1 THR A 40 TYR A 52 1 13 HELIX 2 AA2 GLY A 53 ARG A 61 1 9 HELIX 3 AA3 LEU A 67 SER A 79 1 13 HELIX 4 AA4 ASP A 87 ARG A 95 1 9 HELIX 5 AA5 PRO A 133 ALA A 150 1 18 HELIX 6 AA6 LEU A 220 LEU A 232 1 13 HELIX 7 AA7 HIS A 257 HIS A 266 1 10 HELIX 8 AA8 ASP B 41 TYR B 52 1 12 HELIX 9 AA9 GLY B 68 LEU B 78 1 11 HELIX 10 AB1 ASP B 87 THR B 96 1 10 HELIX 11 AB2 PRO B 133 ALA B 150 1 18 HELIX 12 AB3 LEU B 220 LEU B 232 1 13 HELIX 13 AB4 HIS B 257 GLY B 269 1 13 SHEET 1 AA1 5 THR A 155 ARG A 158 0 SHEET 2 AA1 5 ASN A 120 ILE A 125 1 N ILE A 121 O THR A 155 SHEET 3 AA1 5 ILE A 166 GLY A 171 1 O ILE A 166 N THR A 122 SHEET 4 AA1 5 ALA A 202 ASP A 205 1 O PHE A 204 N GLN A 169 SHEET 5 AA1 5 ALA A 189 ALA A 191 -1 N HIS A 190 O HIS A 203 SHEET 1 AA2 2 TRP A 210 SER A 211 0 SHEET 2 AA2 2 TYR A 218 SER A 219 1 O TYR A 218 N SER A 211 SHEET 1 AA3 5 THR B 155 VAL B 159 0 SHEET 2 AA3 5 ASN B 120 ILE B 125 1 N TYR B 123 O VAL B 159 SHEET 3 AA3 5 ILE B 166 GLY B 171 1 O ILE B 168 N TRP B 124 SHEET 4 AA3 5 ALA B 202 ASP B 205 1 O PHE B 204 N GLN B 169 SHEET 5 AA3 5 ALA B 189 ALA B 191 -1 N HIS B 190 O HIS B 203 SHEET 1 AA4 2 TRP B 210 SER B 211 0 SHEET 2 AA4 2 TYR B 218 SER B 219 1 O TYR B 218 N SER B 211 LINK SG CYS A 99 ZN ZN A 301 1555 1555 2.21 LINK OD2 ASP A 131 CA CA A 304 1555 1555 2.26 LINK O ASP A 165 CA CA A 305 1555 1555 2.20 LINK NE2 HIS A 175 ZN ZN A 302 1555 1555 2.13 LINK OD2 ASP A 177 ZN ZN A 302 1555 1555 1.82 LINK OD1 ASP A 182 CA CA A 303 1555 1555 2.31 LINK O GLY A 183 CA CA A 303 1555 1555 2.41 LINK O ASP A 185 CA CA A 303 1555 1555 2.21 LINK O LEU A 187 CA CA A 303 1555 1555 2.31 LINK NE2 HIS A 190 ZN ZN A 302 1555 1555 2.11 LINK O GLY A 197 CA CA A 305 1555 1555 2.15 LINK O GLN A 199 CA CA A 305 1555 1555 2.32 LINK OD1 ASP A 201 CA CA A 305 1555 1555 2.46 LINK ND1 HIS A 203 ZN ZN A 302 1555 1555 2.01 LINK OD2 ASP A 205 CA CA A 303 1555 1555 2.27 LINK O ASP A 206 CA CA A 304 1555 1555 2.20 LINK OD1 ASP A 206 CA CA A 304 1555 1555 2.35 LINK OE2 GLU A 208 CA CA A 303 1555 1555 2.23 LINK O GLU A 208 CA CA A 304 1555 1555 2.43 LINK NE2 HIS A 226 ZN ZN A 301 1555 1555 2.08 LINK NE2 HIS A 230 ZN ZN A 301 1555 1555 1.97 LINK NE2 HIS A 236 ZN ZN A 301 1555 1555 2.06 LINK SG CYS B 99 ZN ZN B 301 1555 1555 2.09 LINK OD2 ASP B 131 CA CA B 304 1555 1555 2.40 LINK O ASP B 165 CA CA B 305 1555 1555 2.33 LINK NE2 HIS B 175 ZN ZN B 302 1555 1555 2.05 LINK OD2 ASP B 177 ZN ZN B 302 1555 1555 1.96 LINK OD1 ASP B 182 CA CA B 303 1555 1555 2.24 LINK O GLY B 183 CA CA B 303 1555 1555 2.30 LINK O ASP B 185 CA CA B 303 1555 1555 2.20 LINK O LEU B 187 CA CA B 303 1555 1555 2.18 LINK NE2 HIS B 190 ZN ZN B 302 1555 1555 1.98 LINK O GLY B 197 CA CA B 305 1555 1555 2.39 LINK O GLN B 199 CA CA B 305 1555 1555 2.14 LINK OD1 ASP B 201 CA CA B 305 1555 1555 2.41 LINK ND1 HIS B 203 ZN ZN B 302 1555 1555 2.06 LINK OD2 ASP B 205 CA CA B 303 1555 1555 2.17 LINK O ASP B 206 CA CA B 304 1555 1555 2.38 LINK OD1 ASP B 206 CA CA B 304 1555 1555 2.64 LINK OE2 GLU B 208 CA CA B 303 1555 1555 2.32 LINK O GLU B 208 CA CA B 304 1555 1555 2.29 LINK NE2 HIS B 226 ZN ZN B 301 1555 1555 2.07 LINK NE2 HIS B 230 ZN ZN B 301 1555 1555 2.07 LINK NE2 HIS B 236 ZN ZN B 301 1555 1555 1.84 LINK CA CA B 305 O HOH B 413 1555 1555 2.24 LINK CA CA B 305 O HOH B 430 1555 1555 2.13 CRYST1 90.319 73.002 75.994 90.00 102.57 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 0.011072 0.000000 0.002468 0.00000 SCALE2 0.000000 0.013698 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013482 0.00000