10 20 30 40 50 60 70 80 4H3X - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE/HYDROLASE INHIBITOR 14-SEP-12 4H3X
TITLE CRYSTAL STRUCTURE OF AN MMP BROAD SPECTRUM HYDROXAMATE BASED INHIBITOR TITLE 2 CC27 IN COMPLEX WITH THE MMP-9 CATALYTIC DOMAIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: MATRIX METALLOPROTEINASE-9; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: HUMAN WILD-TYPE MMP-9 CATALYTIC DOMAIN UNP RESIDUES 107- COMPND 5 215/391-443; COMPND 6 SYNONYM: MMP-9,92 KDA GELATINASE,92 KDA TYPE IV COLLAGENASE, COMPND 7 GELATINASE B,GELB; COMPND 8 EC: 3.4.24.35,3.4.24.35; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MMP9, CLG4B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3 STAR); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PT7 PROMOTER; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-14B
KEYWDS HYDROLASE/HYDROXAMATE INHIBITOR, ZINCIN-LIKE, GELATINASE, COLLAGENASE KEYWDS 2 (CATALYTIC DOMAIN), HYDROLASE-HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR E.A.STURA,L.VERA,E.CASSAR-LAJEUNESSE,E.NUTI,V.DIVE,A.ROSSELLO
REVDAT 5 31-MAY-17 4H3X 1 COMPND REMARK DBREF REVDAT 4 12-AUG-15 4H3X 1 JRNL REVDAT 3 08-OCT-14 4H3X 1 AUTHOR REVDAT 2 01-MAY-13 4H3X 1 AUTHOR REVDAT 1 24-APR-13 4H3X 0
JRNL AUTH C.ANTONI,L.VERA,L.DEVEL,M.P.CATALANI,B.CZARNY, JRNL AUTH 2 E.CASSAR-LAJEUNESSE,E.NUTI,A.ROSSELLO,V.DIVE,E.A.STURA JRNL TITL CRYSTALLIZATION OF BI-FUNCTIONAL LIGAND PROTEIN COMPLEXES. JRNL REF J.STRUCT.BIOL. V. 182 246 2013 JRNL REFN ISSN 1047-8477 JRNL PMID 23567804 JRNL DOI 10.1016/J.JSB.2013.03.015
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.ANTONI,L.VERA,L.DEVEL,M.P.CATALANI,B.CZARNY, REMARK 1 AUTH 2 E.CASSAR-LAJEUNESSE,E.NUTI,A.ROSSELLO,V.DIVE,E.A.STURA REMARK 1 TITL CRYSTALLIZATION OF BI-FUNCTIONAL LIGAND PROTEIN COMPLEXES. REMARK 1 REF J.STRUCT.BIOL. 2013 REMARK 1 REFN ESSN 1095-8657 REMARK 1 PMID 23567804 REMARK 1 DOI 10.1016/J.JSB.2013.03.015
REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 31949 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1598 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 42.8181 - 3.9226 1.00 2837 150 0.1892 0.2333 REMARK 3 2 3.9226 - 3.1138 1.00 2807 148 0.1764 0.2212 REMARK 3 3 3.1138 - 2.7203 0.99 2776 146 0.1961 0.2836 REMARK 3 4 2.7203 - 2.4716 0.99 2789 146 0.1991 0.2359 REMARK 3 5 2.4716 - 2.2944 0.99 2762 146 0.1969 0.3139 REMARK 3 6 2.2944 - 2.1592 0.99 2788 147 0.1984 0.2603 REMARK 3 7 2.1592 - 2.0510 0.99 2769 145 0.1875 0.2380 REMARK 3 8 2.0510 - 1.9618 0.98 2748 145 0.2000 0.2444 REMARK 3 9 1.9618 - 1.8862 0.99 2754 145 0.2077 0.2585 REMARK 3 10 1.8862 - 1.8211 0.98 2723 143 0.2343 0.3088 REMARK 3 11 1.8211 - 1.7642 0.92 2598 137 0.2696 0.3117 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2957 REMARK 3 ANGLE : 1.030 4030 REMARK 3 CHIRALITY : 0.074 385 REMARK 3 PLANARITY : 0.006 533 REMARK 3 DIHEDRAL : 18.451 1069 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 4H3X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000074987.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : HORIZONTALLY DIFFRACTING SI REMARK 200 (111) MONOCHROMATOR AND PT REMARK 200 COATED MIRRORS IN KIRKPATRICK- REMARK 200 BAEZ GEOMETRY FOR FOCUSING REMARK 200 OPTICS : BENT CYLINDRICAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31957 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 4.230 REMARK 200 R MERGE (I) : 0.13600 REMARK 200 R SYM (I) : 0.11900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.4100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.13 REMARK 200 R MERGE FOR SHELL (I) : 0.66600 REMARK 200 R SYM FOR SHELL (I) : 0.58200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.330 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4H2E REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: HMMP-9-WT 5.5 MG/ML 120 MILLI REMARK 280 -M ACETOHYDROXAMIC ACID. RESERVOIR: 10% PEG 20,000, 60MM MES PH REMARK 280 5.5 + 18% MPEG 5,000, 0.08 M IMIDAZOLE PIPERIDINE; PH 8.5, 0.05 REMARK 280 M NACL. CRYOPROTECTANT: 10% DI-ETHYLENE GLYCOL, 10% 1.2- REMARK 280 PROPANEDIOL, 10% GLYCEROL, 10% PEG 10K, 10% PCTP 50/50, 200MM REMARK 280 NACL , VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, PH 7.0
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 48.97000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA.
REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 173 -136.51 46.04 REMARK 500 ASP A 185 -168.07 65.44 REMARK 500 PRO A 246 48.68 -83.44 REMARK 500 PRO A 246 48.87 -83.44 REMARK 500 ALA B 173 -141.01 57.61 REMARK 500 ASP B 185 -166.37 62.72 REMARK 500 PRO B 246 49.34 -75.82 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 552 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH B 474 DISTANCE = 7.22 ANGSTROMS REMARK 525 HOH B 510 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH B 555 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH B 557 DISTANCE = 8.04 ANGSTROMS REMARK 525 HOH B 558 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH B 562 DISTANCE = 6.76 ANGSTROMS REMARK 525 HOH B 570 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH B 580 DISTANCE = 6.46 ANGSTROMS
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 190 NE2 REMARK 620 2 HIS A 203 ND1 110.7 REMARK 620 3 ASP A 177 OD1 113.6 91.7 REMARK 620 4 HIS A 175 NE2 115.1 107.1 115.8 REMARK 620 N 1 2 3 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 ASP B 177 OD1 REMARK 620 2 HIS B 203 ND1 95.8 REMARK 620 3 HIS B 190 NE2 112.0 109.4 REMARK 620 4 HIS B 175 NE2 118.2 115.6 105.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 226 NE2 REMARK 620 2 10B A 306 O7 99.1 REMARK 620 3 HIS A 230 NE2 95.3 94.9 REMARK 620 4 HIS A 236 NE2 104.7 154.5 91.8 REMARK 620 5 10B A 306 O2 152.3 73.8 111.9 80.9 REMARK 620 N 1 2 3 4 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 236 NE2 REMARK 620 2 HIS B 230 NE2 96.3 REMARK 620 3 HIS B 226 NE2 105.0 93.7 REMARK 620 4 10B B 306 O2 82.4 130.8 134.4 REMARK 620 5 10B B 306 O7 152.8 96.3 98.1 71.1 REMARK 620 N 1 2 3 4 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 GLU B 208 OE2 REMARK 620 2 LEU B 187 O 84.8 REMARK 620 3 ASP B 205 OD2 103.6 90.0 REMARK 620 4 GLY B 183 O 90.5 175.1 92.1 REMARK 620 5 ASP B 182 OD1 165.5 95.0 90.9 89.3 REMARK 620 6 ASP B 185 O 82.8 94.3 172.6 84.0 82.7 REMARK 620 N 1 2 3 4 5 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 205 OD2 REMARK 620 2 GLU A 208 OE2 97.7 REMARK 620 3 GLY A 183 O 89.8 82.6 REMARK 620 4 ASP A 182 OD1 93.2 165.0 87.1 REMARK 620 5 LEU A 187 O 89.9 95.7 178.2 94.7 REMARK 620 6 ASP A 185 O 176.7 80.0 87.5 88.7 92.7 REMARK 620 N 1 2 3 4 5 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 HOH B 401 O REMARK 620 2 ASP B 165 O 86.7 REMARK 620 3 HOH B 405 O 93.2 90.2 REMARK 620 4 ASP B 201 OD1 172.6 89.6 93.3 REMARK 620 5 GLN B 199 O 74.8 105.0 159.7 100.1 REMARK 620 6 GLY B 197 O 94.5 168.6 78.4 90.4 86.2 REMARK 620 N 1 2 3 4 5 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 206 O REMARK 620 2 ASP A 131 OD2 154.4 REMARK 620 3 GLU A 208 O 86.7 81.6 REMARK 620 4 HOH A 453 O 99.4 100.5 78.4 REMARK 620 5 ASP A 206 OD1 73.9 89.7 112.5 166.2 REMARK 620 6 HOH A 452 O 74.3 122.7 153.8 86.9 79.7 REMARK 620 7 ASP A 131 OD1 150.8 48.1 122.2 84.3 95.9 77.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 165 O REMARK 620 2 GLY A 197 O 171.0 REMARK 620 3 HOH A 411 O 90.0 91.2 REMARK 620 4 GLN A 199 O 105.0 84.0 81.4 REMARK 620 5 ASP A 201 OD1 89.0 90.6 174.8 93.9 REMARK 620 6 HOH A 406 O 87.7 83.4 91.0 165.2 94.0 REMARK 620 N 1 2 3 4 5 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 GLU B 208 O 78.3 REMARK 620 3 ASP B 206 O 153.3 87.4 REMARK 620 4 ASP B 206 OD1 92.3 105.6 69.8 REMARK 620 5 HOH B 468 O 104.9 176.1 90.5 76.7 REMARK 620 6 HOH B 529 O 107.6 93.0 95.4 155.2 83.9 REMARK 620 7 ASP B 131 OD1 48.4 123.6 148.6 94.7 58.8 88.2 REMARK 620 N 1 2 3 4 5 6
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 10B A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGO A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 313 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 10B B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 309
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4H1Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MUTANT MMP-9 CATALYTIC DOMAIN IN COMPLEX WITH REMARK 900 A TWIN INHIBITOR. REMARK 900 RELATED ID: 4H2E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN MMP TWIN INHIBITOR COMPLEXING TWO MMP-9 REMARK 900 CATALYTIC DOMAINS REMARK 900 RELATED ID: 2OW1 RELATED DB: PDB REMARK 900 MMP-9 ACTIVE SITE MUTANT WITH TRIFLUOROMETHYL HYDROXAMATE INHIBITOR
REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CRYSTALLIZED SEQUENCE CORRESPONDS TO A CHIMERIC CONSTRUCT REMARK 999 OBTAINED BY DELETING THE DOMAIN CORRESPONDING TO UNP RESIDUES 215- REMARK 999 390
DBREF 4H3X A 107 216 UNP P14780 MMP9_HUMAN 107 216 DBREF 4H3X A 217 269 UNP P14780 MMP9_HUMAN 392 444 DBREF 4H3X B 107 216 UNP P14780 MMP9_HUMAN 107 216 DBREF 4H3X B 217 269 UNP P14780 MMP9_HUMAN 392 444
SEQADV 4H3X GLY A 106 UNP P14780 EXPRESSION TAG SEQADV 4H3X GLY B 106 UNP P14780 EXPRESSION TAG
SEQRES 1 A 164 GLY PHE GLN THR PHE GLU GLY ASP LEU LYS TRP HIS HIS SEQRES 2 A 164 HIS ASN ILE THR TYR TRP ILE GLN ASN TYR SER GLU ASP SEQRES 3 A 164 LEU PRO ARG ALA VAL ILE ASP ASP ALA PHE ALA ARG ALA SEQRES 4 A 164 PHE ALA LEU TRP SER ALA VAL THR PRO LEU THR PHE THR SEQRES 5 A 164 ARG VAL TYR SER ARG ASP ALA ASP ILE VAL ILE GLN PHE SEQRES 6 A 164 GLY VAL ALA GLU HIS GLY ASP GLY TYR PRO PHE ASP GLY SEQRES 7 A 164 LYS ASP GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO SEQRES 8 A 164 GLY ILE GLN GLY ASP ALA HIS PHE ASP ASP ASP GLU LEU SEQRES 9 A 164 TRP SER LEU GLY LYS GLY VAL GLY TYR SER LEU PHE LEU SEQRES 10 A 164 VAL ALA ALA HIS GLU PHE GLY HIS ALA LEU GLY LEU ASP SEQRES 11 A 164 HIS SER SER VAL PRO GLU ALA LEU MET TYR PRO MET TYR SEQRES 12 A 164 ARG PHE THR GLU GLY PRO PRO LEU HIS LYS ASP ASP VAL SEQRES 13 A 164 ASN GLY ILE ARG HIS LEU TYR GLY SEQRES 1 B 164 GLY PHE GLN THR PHE GLU GLY ASP LEU LYS TRP HIS HIS SEQRES 2 B 164 HIS ASN ILE THR TYR TRP ILE GLN ASN TYR SER GLU ASP SEQRES 3 B 164 LEU PRO ARG ALA VAL ILE ASP ASP ALA PHE ALA ARG ALA SEQRES 4 B 164 PHE ALA LEU TRP SER ALA VAL THR PRO LEU THR PHE THR SEQRES 5 B 164 ARG VAL TYR SER ARG ASP ALA ASP ILE VAL ILE GLN PHE SEQRES 6 B 164 GLY VAL ALA GLU HIS GLY ASP GLY TYR PRO PHE ASP GLY SEQRES 7 B 164 LYS ASP GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO SEQRES 8 B 164 GLY ILE GLN GLY ASP ALA HIS PHE ASP ASP ASP GLU LEU SEQRES 9 B 164 TRP SER LEU GLY LYS GLY VAL GLY TYR SER LEU PHE LEU SEQRES 10 B 164 VAL ALA ALA HIS GLU PHE GLY HIS ALA LEU GLY LEU ASP SEQRES 11 B 164 HIS SER SER VAL PRO GLU ALA LEU MET TYR PRO MET TYR SEQRES 12 B 164 ARG PHE THR GLU GLY PRO PRO LEU HIS LYS ASP ASP VAL SEQRES 13 B 164 ASN GLY ILE ARG HIS LEU TYR GLY
HET ZN A 301 1 HET ZN A 302 1 HET CA A 303 1 HET CA A 304 1 HET CA A 305 1 HET 10B A 306 25 HET GOL A 307 6 HET GOL A 308 6 HET GOL A 309 6 HET PGO A 310 5 HET GOL A 311 6 HET GOL A 312 6 HET GOL A 313 6 HET ZN B 301 1 HET ZN B 302 1 HET CA B 303 1 HET CA B 304 1 HET CA B 305 1 HET 10B B 306 25 HET GOL B 307 6 HET PEG B 308 7 HET PEG B 309 7
HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM 10B N-2-(BIPHENYL-4-YLSULFONYL)-N-2-(ISOPROPYLOXY)- HETNAM 2 10B ACETOHYDROXAMIC ACID HETNAM GOL GLYCEROL HETNAM PGO S-1,2-PROPANEDIOL HETNAM PEG DI(HYDROXYETHYL)ETHER
HETSYN 10B N~2~-(BIPHENYL-4-YLSULFONYL)-N-HYDROXY-N~2~-(PROPAN-2- HETSYN 2 10B YLOXY)GLYCINAMIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 3 ZN 4(ZN 2+) FORMUL 5 CA 6(CA 2+) FORMUL 8 10B 2(C17 H20 N2 O5 S) FORMUL 9 GOL 7(C3 H8 O3) FORMUL 12 PGO C3 H8 O2 FORMUL 23 PEG 2(C4 H10 O3) FORMUL 25 HOH *380(H2 O)
HELIX 1 1 PRO A 133 VAL A 151 1 19 HELIX 2 2 LEU A 220 LEU A 232 1 13 HELIX 3 3 HIS A 257 GLY A 269 1 13 HELIX 4 4 PRO B 133 ALA B 150 1 18 HELIX 5 5 LEU B 220 GLY B 233 1 14 HELIX 6 6 HIS B 257 GLY B 269 1 13
SHEET 1 A 2 GLN A 108 THR A 109 0 SHEET 2 A 2 LEU A 234 ASP A 235 -1 O ASP A 235 N GLN A 108 SHEET 1 B 5 THR A 155 ARG A 158 0 SHEET 2 B 5 ASN A 120 ILE A 125 1 N ILE A 121 O THR A 157 SHEET 3 B 5 ILE A 166 GLY A 171 1 O ILE A 168 N TRP A 124 SHEET 4 B 5 ALA A 202 ASP A 205 1 O PHE A 204 N GLN A 169 SHEET 5 B 5 ALA A 189 ALA A 191 -1 N HIS A 190 O HIS A 203 SHEET 1 C 2 TRP A 210 SER A 211 0 SHEET 2 C 2 TYR A 218 SER A 219 1 O TYR A 218 N SER A 211 SHEET 1 D 5 THR B 155 ARG B 158 0 SHEET 2 D 5 ASN B 120 ILE B 125 1 N ILE B 121 O THR B 157 SHEET 3 D 5 ILE B 166 GLY B 171 1 O ILE B 168 N TRP B 124 SHEET 4 D 5 ALA B 202 ASP B 205 1 O PHE B 204 N GLN B 169 SHEET 5 D 5 ALA B 189 ALA B 191 -1 N HIS B 190 O HIS B 203 SHEET 1 E 2 TRP B 210 SER B 211 0 SHEET 2 E 2 TYR B 218 SER B 219 1 O TYR B 218 N SER B 211
LINK NE2 HIS A 190 ZN ZN A 302 1555 1555 1.95 LINK OD1 ASP B 177 ZN ZN B 302 1555 1555 1.96 LINK NE2 HIS A 226 ZN ZN A 301 1555 1555 1.97 LINK ND1 HIS A 203 ZN ZN A 302 1555 1555 2.01 LINK ZN ZN A 301 O7 10B A 306 1555 1555 2.01 LINK OD1 ASP A 177 ZN ZN A 302 1555 1555 2.02 LINK ND1 HIS B 203 ZN ZN B 302 1555 1555 2.04 LINK NE2 HIS B 236 ZN ZN B 301 1555 1555 2.09 LINK NE2 HIS B 230 ZN ZN B 301 1555 1555 2.09 LINK NE2 HIS B 190 ZN ZN B 302 1555 1555 2.10 LINK NE2 HIS B 175 ZN ZN B 302 1555 1555 2.11 LINK NE2 HIS A 230 ZN ZN A 301 1555 1555 2.12 LINK NE2 HIS B 226 ZN ZN B 301 1555 1555 2.13 LINK NE2 HIS A 175 ZN ZN A 302 1555 1555 2.16 LINK ZN ZN B 301 O2 10B B 306 1555 1555 2.20 LINK OE2 GLU B 208 CA CA B 303 1555 1555 2.21 LINK NE2 HIS A 236 ZN ZN A 301 1555 1555 2.21 LINK OD2 ASP A 205 CA CA A 303 1555 1555 2.24 LINK OE2 GLU A 208 CA CA A 303 1555 1555 2.25 LINK CA CA B 305 O HOH B 401 1555 1555 2.26 LINK O GLY A 183 CA CA A 303 1555 1555 2.26 LINK ZN ZN B 301 O7 10B B 306 1555 1555 2.30 LINK O ASP A 206 CA CA A 304 1555 1555 2.30 LINK O LEU B 187 CA CA B 303 1555 1555 2.31 LINK OD1 ASP A 182 CA CA A 303 1555 1555 2.31 LINK OD2 ASP B 205 CA CA B 303 1555 1555 2.31 LINK O GLY B 183 CA CA B 303 1555 1555 2.32 LINK O ASP A 165 CA CA A 305 1555 1555 2.32 LINK O ASP B 165 CA CA B 305 1555 1555 2.33 LINK OD2 ASP A 131 CA CA A 304 1555 1555 2.33 LINK O GLY A 197 CA CA A 305 1555 1555 2.33 LINK O LEU A 187 CA CA A 303 1555 1555 2.34 LINK O ASP A 185 CA CA A 303 1555 1555 2.34 LINK CA CA A 305 O HOH A 411 1555 1555 2.34 LINK O GLU A 208 CA CA A 304 1555 1555 2.35 LINK O GLN A 199 CA CA A 305 1555 1555 2.35 LINK OD1 ASP A 201 CA CA A 305 1555 1555 2.35 LINK OD2 ASP B 131 CA CA B 304 1555 1555 2.36 LINK ZN ZN A 301 O2 10B A 306 1555 1555 2.36 LINK O GLU B 208 CA CA B 304 1555 1555 2.40 LINK CA CA A 304 O HOH A 453 1555 1555 2.40 LINK CA CA B 305 O HOH B 405 1555 1555 2.41 LINK OD1 ASP B 201 CA CA B 305 1555 1555 2.41 LINK OD1 ASP A 206 CA CA A 304 1555 1555 2.41 LINK OD1 ASP B 182 CA CA B 303 1555 1555 2.42 LINK O ASP B 185 CA CA B 303 1555 1555 2.42 LINK CA CA A 305 O HOH A 406 1555 1555 2.43 LINK O ASP B 206 CA CA B 304 1555 1555 2.43 LINK O GLN B 199 CA CA B 305 1555 1555 2.44 LINK OD1 ASP B 206 CA CA B 304 1555 1555 2.47 LINK O GLY B 197 CA CA B 305 1555 1555 2.47 LINK CA CA B 304 O HOH B 468 1555 1555 2.48 LINK CA CA B 304 O HOH B 529 1555 1555 2.49 LINK CA CA A 304 O HOH A 452 1555 1555 2.51 LINK OD1 ASP B 131 CA CA B 304 1555 1555 2.87 LINK OD1 ASP A 131 CA CA A 304 1555 1555 2.90
SITE 1 AC1 4 HIS A 226 HIS A 230 HIS A 236 10B A 306 SITE 1 AC2 4 HIS A 175 ASP A 177 HIS A 190 HIS A 203 SITE 1 AC3 6 ASP A 182 GLY A 183 ASP A 185 LEU A 187 SITE 2 AC3 6 ASP A 205 GLU A 208 SITE 1 AC4 5 ASP A 131 ASP A 206 GLU A 208 HOH A 452 SITE 2 AC4 5 HOH A 453 SITE 1 AC5 6 ASP A 165 GLY A 197 GLN A 199 ASP A 201 SITE 2 AC5 6 HOH A 406 HOH A 411 SITE 1 AC6 17 GLY A 186 LEU A 187 LEU A 188 ALA A 189 SITE 2 AC6 17 LEU A 222 HIS A 226 GLU A 227 HIS A 230 SITE 3 AC6 17 HIS A 236 LEU A 243 TYR A 245 MET A 247 SITE 4 AC6 17 ZN A 301 HOH A 415 HOH A 492 TYR B 245 SITE 5 AC6 17 PRO B 246 SITE 1 AC7 6 PRO A 254 HOH A 421 PRO B 254 PRO B 255 SITE 2 AC7 6 HOH B 448 HOH B 451 SITE 1 AC8 9 ASP A 177 GLY A 178 GOL A 311 HOH A 476 SITE 2 AC8 9 HOH A 515 HOH A 553 HOH A 559 HOH A 560 SITE 3 AC8 9 HOH A 590 SITE 1 AC9 7 TYR A 179 LEU A 187 HIS A 190 HOH A 594 SITE 2 AC9 7 HOH A 595 PRO B 240 TYR B 245 SITE 1 BC1 2 ALA A 173 GLU A 174 SITE 1 BC2 5 GOL A 308 HOH A 480 HOH A 515 HOH A 529 SITE 2 BC2 5 HOH A 553 SITE 1 BC3 4 ASN A 120 THR A 122 THR A 157 HOH A 536 SITE 1 BC4 2 HOH A 434 HOH A 483 SITE 1 BC5 4 HIS B 226 HIS B 230 HIS B 236 10B B 306 SITE 1 BC6 4 HIS B 175 ASP B 177 HIS B 190 HIS B 203 SITE 1 BC7 6 ASP B 182 GLY B 183 ASP B 185 LEU B 187 SITE 2 BC7 6 ASP B 205 GLU B 208 SITE 1 BC8 5 ASP B 131 ASP B 206 GLU B 208 HOH B 468 SITE 2 BC8 5 HOH B 529 SITE 1 BC9 6 ASP B 165 GLY B 197 GLN B 199 ASP B 201 SITE 2 BC9 6 HOH B 401 HOH B 405 SITE 1 CC1 18 TYR A 245 PRO A 246 MET A 247 GLY B 186 SITE 2 CC1 18 LEU B 187 LEU B 188 ALA B 189 LEU B 222 SITE 3 CC1 18 HIS B 226 GLU B 227 HIS B 230 HIS B 236 SITE 4 CC1 18 LEU B 243 TYR B 245 MET B 247 TYR B 248 SITE 5 CC1 18 ZN B 301 HOH B 444 SITE 1 CC2 5 PHE B 250 THR B 251 HOH B 423 HOH B 515 SITE 2 CC2 5 HOH B 546 SITE 1 CC3 4 PEG B 309 HOH B 442 HOH B 443 HOH B 480 SITE 1 CC4 3 TYR B 179 PEG B 308 HOH B 442
CRYST1 40.110 97.940 46.080 90.00 111.73 90.00 P 1 21 1 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.024931 0.000000 0.009937 0.00000
SCALE2 0.000000 0.010210 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023361 0.00000