HEADER HYDROLASE/HYDROLASE INHIBITOR 13-SEP-12 4H30 TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-12 IN COMPLEX WITH A TITLE 2 TWIN INHIBITOR. COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACROPHAGE METALLOELASTASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: HUMAN MMP12 CATALYTIC DOMAIN (UNP RESIDUES 106-263); COMPND 5 SYNONYM: MME, MACROPHAGE ELASTASE, ME, HME, MATRIX METALLOPROTEINASE- COMPND 6 12, MMP-12; COMPND 7 EC: 3.4.24.65; COMPND 8 ENGINEERED: YES; COMPND 9 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: HME, MMP12; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24A KEYWDS DIVALENT INHIBITOR, CARBOXYLIC TWIN INHIBITOR, DIMERISATION, KEYWDS 2 METZINCIN, ZINC PROTEASE, HYDROLASE-HYDROLASE INHIBTIOR COMPLEX, KEYWDS 3 HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.ANTONI,E.A.STURA,L.VERA,E.NUTI,L.CARAFA,E.CASSAR-LAJEUNESSE,V.DIVE, AUTHOR 2 A.ROSSELLO REVDAT 5 20-SEP-23 4H30 1 REMARK SEQADV LINK REVDAT 4 12-AUG-15 4H30 1 JRNL REVDAT 3 08-OCT-14 4H30 1 AUTHOR REVDAT 2 01-MAY-13 4H30 1 AUTHOR REVDAT 1 24-APR-13 4H30 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 2 REMARK 2 RESOLUTION. 1.43 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) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 61749 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3087 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 43.3202 - 3.9904 0.99 2873 151 0.1613 0.1585 REMARK 3 2 3.9904 - 3.1676 1.00 2760 145 0.1405 0.1629 REMARK 3 3 3.1676 - 2.7672 1.00 2698 142 0.1588 0.1807 REMARK 3 4 2.7672 - 2.5143 1.00 2719 143 0.1568 0.1579 REMARK 3 5 2.5143 - 2.3341 1.00 2679 141 0.1566 0.1812 REMARK 3 6 2.3341 - 2.1965 1.00 2692 142 0.1523 0.1764 REMARK 3 7 2.1965 - 2.0865 1.00 2673 140 0.1441 0.1709 REMARK 3 8 2.0865 - 1.9956 1.00 2650 140 0.1411 0.1846 REMARK 3 9 1.9956 - 1.9188 1.00 2678 141 0.1487 0.1632 REMARK 3 10 1.9188 - 1.8526 1.00 2662 140 0.1463 0.1757 REMARK 3 11 1.8526 - 1.7947 1.00 2652 140 0.1551 0.1896 REMARK 3 12 1.7947 - 1.7434 1.00 2663 140 0.1555 0.1849 REMARK 3 13 1.7434 - 1.6975 1.00 2673 140 0.1571 0.1890 REMARK 3 14 1.6975 - 1.6561 1.00 2615 138 0.1600 0.2138 REMARK 3 15 1.6561 - 1.6184 1.00 2630 138 0.1642 0.1744 REMARK 3 16 1.6184 - 1.5840 1.00 2636 139 0.1667 0.2120 REMARK 3 17 1.5840 - 1.5523 1.00 2665 141 0.1702 0.2023 REMARK 3 18 1.5523 - 1.5230 1.00 2639 138 0.1799 0.2021 REMARK 3 19 1.5230 - 1.4958 1.00 2642 139 0.1857 0.2159 REMARK 3 20 1.4958 - 1.4704 1.00 2628 139 0.1968 0.2057 REMARK 3 21 1.4704 - 1.4467 1.00 2675 141 0.2062 0.2565 REMARK 3 22 1.4467 - 1.4244 0.94 2460 129 0.2270 0.2230 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.62 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 : 0.006 2857 REMARK 3 ANGLE : 1.118 3876 REMARK 3 CHIRALITY : 0.078 382 REMARK 3 PLANARITY : 0.006 509 REMARK 3 DIHEDRAL : 16.272 1012 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 4H30 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_1000074954. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8856 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61752 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.820 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : 0.05300 REMARK 200 FOR THE DATA SET : 19.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.62600 REMARK 200 R SYM FOR SHELL (I) : 0.57000 REMARK 200 FOR SHELL : 2.770 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: 4EFS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: HMMP12 F171D AT 0.36 MILLI-M REMARK 280 + 0.001 M AHA. RESERVOIR: 13% PEG 20,000 0.2 M IMIDAZOLE MALATE REMARK 280 0.05 M NACL CRYOPROTECTANT: 27% PEG 8,000 15% MPEG 550, 10% REMARK 280 GLYCEROL, 0.09 M TRIS-HCL , PH 8.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.45500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.28000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.87500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.28000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.45500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.87500 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: 4250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -97.0 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 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 HIS A 206 -123.86 -126.34 REMARK 500 SER A 207 -164.78 -100.68 REMARK 500 PRO A 238 35.27 -82.20 REMARK 500 ARG B 110 41.16 -93.37 REMARK 500 ARG B 110 39.70 -93.60 REMARK 500 ARG B 110 42.09 -94.06 REMARK 500 ARG B 110 39.66 -92.68 REMARK 500 HIS B 206 -127.99 -128.13 REMARK 500 HIS B 206 -136.71 -128.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 124 OD2 REMARK 620 2 ASP A 124 OD1 51.3 REMARK 620 3 GLU A 199 O 140.4 160.3 REMARK 620 4 GLU A 199 OE2 87.6 87.4 78.7 REMARK 620 5 GLU A 201 O 77.5 122.0 77.3 119.0 REMARK 620 6 HOH A 404 O 136.0 85.0 80.4 86.4 141.4 REMARK 620 7 HOH A 405 O 98.3 83.7 105.8 162.6 78.4 77.9 REMARK 620 N 1 2 3 4 5 6 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 158 O REMARK 620 2 GLY A 190 O 167.2 REMARK 620 3 GLY A 192 O 95.0 93.3 REMARK 620 4 ASP A 194 OD1 87.9 102.1 87.9 REMARK 620 5 HOH A 416 O 82.8 89.2 79.8 163.8 REMARK 620 6 HOH A 424 O 86.4 83.9 171.6 100.4 92.2 REMARK 620 N 1 2 3 4 5 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 168 NE2 REMARK 620 2 ASP A 170 OD2 108.0 REMARK 620 3 HIS A 183 NE2 116.1 115.6 REMARK 620 4 HIS A 196 ND1 106.9 94.9 113.0 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 175 OD1 REMARK 620 2 GLY A 176 O 88.0 REMARK 620 3 GLY A 178 O 86.5 85.2 REMARK 620 4 ILE A 180 O 90.9 178.9 95.1 REMARK 620 5 ASP A 198 OD2 92.3 87.3 172.4 92.4 REMARK 620 6 GLU A 201 OE2 168.0 89.2 81.7 91.8 99.2 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 218 NE2 REMARK 620 2 HIS A 222 NE2 102.9 REMARK 620 3 HIS A 228 NE2 113.4 103.0 REMARK 620 4 0ZD B 306 O22 112.9 124.9 99.4 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 124 OD2 REMARK 620 2 ASP B 124 OD1 50.2 REMARK 620 3 GLU B 199 O 142.7 159.1 REMARK 620 4 GLU B 199 OE2 87.9 88.4 77.6 REMARK 620 5 GLU B 201 O 77.2 121.3 79.3 117.2 REMARK 620 6 HOH B 407 O 133.0 82.9 80.9 87.1 144.0 REMARK 620 7 HOH B 408 O 103.0 86.5 101.5 160.7 81.1 73.8 REMARK 620 N 1 2 3 4 5 6 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 158 O REMARK 620 2 GLY B 190 O 161.4 REMARK 620 3 GLY B 192 O 92.7 99.1 REMARK 620 4 ASP B 194 OD1 89.9 103.1 95.6 REMARK 620 5 HOH B 442 O 85.6 81.4 84.2 175.5 REMARK 620 N 1 2 3 4 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 168 NE2 REMARK 620 2 ASP B 170 OD2 105.6 REMARK 620 3 HIS B 183 NE2 113.4 120.5 REMARK 620 4 HIS B 183 NE2 115.6 119.5 2.2 REMARK 620 5 HIS B 196 ND1 110.6 93.9 111.2 109.6 REMARK 620 N 1 2 3 4 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 175 OD1 REMARK 620 2 GLY B 176 O 87.0 REMARK 620 3 GLY B 178 O 83.9 86.7 REMARK 620 4 ILE B 180 O 93.5 179.5 93.5 REMARK 620 5 ASP B 198 OD2 94.5 88.9 175.4 90.9 REMARK 620 6 GLU B 201 OE2 164.2 89.9 80.5 89.7 100.9 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 218 NE2 REMARK 620 2 HIS B 222 NE2 102.3 REMARK 620 3 HIS B 228 NE2 113.7 103.8 REMARK 620 4 0ZD B 306 O62 115.2 123.3 98.3 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 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 GOL 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 GOL 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 ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0ZD B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 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: 4H2E 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: 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: 4EFS RELATED DB: PDB REMARK 900 HUMAN MMP12 IN COMPLEX WITH L-GLUTAMATE MOTIF INHIBITOR. REMARK 900 RELATED ID: 3LIR RELATED DB: PDB REMARK 900 HUMAN MMP12 IN COMPLEX WITH NON-ZINC CHELATING INHIBITOR. REMARK 900 RELATED ID: 4H3X RELATED DB: PDB DBREF 4H30 A 106 263 UNP P39900 MMP12_HUMAN 106 263 DBREF 4H30 B 106 263 UNP P39900 MMP12_HUMAN 106 263 SEQADV 4H30 MET A 105 UNP P39900 EXPRESSION TAG SEQADV 4H30 ASP A 171 UNP P39900 PHE 171 ENGINEERED MUTATION SEQADV 4H30 MET B 105 UNP P39900 EXPRESSION TAG SEQADV 4H30 ASP B 171 UNP P39900 PHE 171 ENGINEERED MUTATION SEQRES 1 A 159 MET GLY PRO VAL TRP ARG LYS HIS TYR ILE THR TYR ARG SEQRES 2 A 159 ILE ASN ASN TYR THR PRO ASP MET ASN ARG GLU ASP VAL SEQRES 3 A 159 ASP TYR ALA ILE ARG LYS ALA PHE GLN VAL TRP SER ASN SEQRES 4 A 159 VAL THR PRO LEU LYS PHE SER LYS ILE ASN THR GLY MET SEQRES 5 A 159 ALA ASP ILE LEU VAL VAL PHE ALA ARG GLY ALA HIS GLY SEQRES 6 A 159 ASP ASP HIS ALA PHE ASP GLY LYS GLY GLY ILE LEU ALA SEQRES 7 A 159 HIS ALA PHE GLY PRO GLY SER GLY ILE GLY GLY ASP ALA SEQRES 8 A 159 HIS PHE ASP GLU ASP GLU PHE TRP THR THR HIS SER GLY SEQRES 9 A 159 GLY THR ASN LEU PHE LEU THR ALA VAL HIS GLU ILE GLY SEQRES 10 A 159 HIS SER LEU GLY LEU GLY HIS SER SER ASP PRO LYS ALA SEQRES 11 A 159 VAL MET PHE PRO THR TYR LYS TYR VAL ASP ILE ASN THR SEQRES 12 A 159 PHE ARG LEU SER ALA ASP ASP ILE ARG GLY ILE GLN SER SEQRES 13 A 159 LEU TYR GLY SEQRES 1 B 159 MET GLY PRO VAL TRP ARG LYS HIS TYR ILE THR TYR ARG SEQRES 2 B 159 ILE ASN ASN TYR THR PRO ASP MET ASN ARG GLU ASP VAL SEQRES 3 B 159 ASP TYR ALA ILE ARG LYS ALA PHE GLN VAL TRP SER ASN SEQRES 4 B 159 VAL THR PRO LEU LYS PHE SER LYS ILE ASN THR GLY MET SEQRES 5 B 159 ALA ASP ILE LEU VAL VAL PHE ALA ARG GLY ALA HIS GLY SEQRES 6 B 159 ASP ASP HIS ALA PHE ASP GLY LYS GLY GLY ILE LEU ALA SEQRES 7 B 159 HIS ALA PHE GLY PRO GLY SER GLY ILE GLY GLY ASP ALA SEQRES 8 B 159 HIS PHE ASP GLU ASP GLU PHE TRP THR THR HIS SER GLY SEQRES 9 B 159 GLY THR ASN LEU PHE LEU THR ALA VAL HIS GLU ILE GLY SEQRES 10 B 159 HIS SER LEU GLY LEU GLY HIS SER SER ASP PRO LYS ALA SEQRES 11 B 159 VAL MET PHE PRO THR TYR LYS TYR VAL ASP ILE ASN THR SEQRES 12 B 159 PHE ARG LEU SER ALA ASP ASP ILE ARG GLY ILE GLN SER SEQRES 13 B 159 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 GOL A 306 6 HET GOL A 307 6 HET GOL A 308 6 HET GOL A 309 6 HET GOL A 310 6 HET GOL A 311 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 0ZD B 306 62 HET GOL B 307 6 HET GOL B 308 6 HET PEG B 309 7 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETNAM 0ZD N,N'-BIS(2-[(BIPHENYL-4YLSULFONYL)[(2R)-1-HYDROXY-3- HETNAM 2 0ZD METHYL-1-OXOBUTAN-2-YL]-AMINO]ETHYL)BENZENE-1,3- HETNAM 3 0ZD DICARBOXAMIDE HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN 4(ZN 2+) FORMUL 5 CA 6(CA 2+) FORMUL 8 GOL 8(C3 H8 O3) FORMUL 19 0ZD C46 H50 N4 O10 S2 FORMUL 22 PEG C4 H10 O3 FORMUL 23 HOH *457(H2 O) HELIX 1 1 ASN A 126 ASN A 143 1 18 HELIX 2 2 LEU A 212 LEU A 224 1 13 HELIX 3 3 SER A 251 TYR A 262 1 12 HELIX 4 4 ASN B 126 ASN B 143 1 18 HELIX 5 5 LEU B 212 LEU B 224 1 13 HELIX 6 6 SER B 251 GLY B 263 1 13 SHEET 1 A 5 LYS A 148 LYS A 151 0 SHEET 2 A 5 TYR A 113 ILE A 118 1 N ILE A 114 O LYS A 148 SHEET 3 A 5 ILE A 159 ALA A 164 1 O VAL A 161 N ARG A 117 SHEET 4 A 5 ALA A 195 ASP A 198 1 O PHE A 197 N VAL A 162 SHEET 5 A 5 ALA A 182 ALA A 184 -1 N HIS A 183 O HIS A 196 SHEET 1 B 2 TRP A 203 THR A 204 0 SHEET 2 B 2 THR A 210 ASN A 211 1 O THR A 210 N THR A 204 SHEET 1 C 5 LYS B 148 LYS B 151 0 SHEET 2 C 5 TYR B 113 ILE B 118 1 N ILE B 114 O LYS B 148 SHEET 3 C 5 ILE B 159 ALA B 164 1 O VAL B 161 N ARG B 117 SHEET 4 C 5 ALA B 195 ASP B 198 1 O PHE B 197 N VAL B 162 SHEET 5 C 5 ALA B 182 ALA B 184 -1 N HIS B 183 O HIS B 196 SHEET 1 D 2 TRP B 203 THR B 204 0 SHEET 2 D 2 THR B 210 ASN B 211 1 O THR B 210 N THR B 204 LINK OD2 ASP A 124 CA CA A 304 1555 1555 2.35 LINK OD1 ASP A 124 CA CA A 304 1555 1555 2.67 LINK O ASP A 158 CA CA A 303 1555 1555 2.30 LINK NE2 HIS A 168 ZN ZN A 302 1555 1555 2.00 LINK OD2 ASP A 170 ZN ZN A 302 1555 1555 1.87 LINK OD1 ASP A 175 CA CA A 305 1555 1555 2.38 LINK O GLY A 176 CA CA A 305 1555 1555 2.31 LINK O GLY A 178 CA CA A 305 1555 1555 2.35 LINK O ILE A 180 CA CA A 305 1555 1555 2.29 LINK NE2 HIS A 183 ZN ZN A 302 1555 1555 1.98 LINK O GLY A 190 CA CA A 303 1555 1555 2.29 LINK O GLY A 192 CA CA A 303 1555 1555 2.28 LINK OD1 ASP A 194 CA CA A 303 1555 1555 2.42 LINK ND1 HIS A 196 ZN ZN A 302 1555 1555 2.03 LINK OD2 ASP A 198 CA CA A 305 1555 1555 2.31 LINK O GLU A 199 CA CA A 304 1555 1555 2.31 LINK OE2 GLU A 199 CA CA A 304 1555 1555 2.38 LINK O GLU A 201 CA CA A 304 1555 1555 2.42 LINK OE2 GLU A 201 CA CA A 305 1555 1555 2.29 LINK NE2 HIS A 218 ZN ZN A 301 1555 1555 2.02 LINK NE2 HIS A 222 ZN ZN A 301 1555 1555 2.03 LINK NE2 HIS A 228 ZN ZN A 301 1555 1555 2.01 LINK ZN ZN A 301 O22 0ZD B 306 1555 1555 1.86 LINK CA CA A 303 O HOH A 416 1555 1555 2.40 LINK CA CA A 303 O HOH A 424 1555 1555 2.35 LINK CA CA A 304 O HOH A 404 1555 1555 2.48 LINK CA CA A 304 O HOH A 405 1555 1555 2.36 LINK OD2 ASP B 124 CA CA B 304 1555 1555 2.43 LINK OD1 ASP B 124 CA CA B 304 1555 1555 2.69 LINK O ASP B 158 CA CA B 303 1555 1555 2.28 LINK NE2 HIS B 168 ZN ZN B 302 1555 1555 2.00 LINK OD2 ASP B 170 ZN ZN B 302 1555 1555 1.92 LINK OD1 ASP B 175 CA CA B 305 1555 1555 2.43 LINK O GLY B 176 CA CA B 305 1555 1555 2.31 LINK O GLY B 178 CA CA B 305 1555 1555 2.36 LINK O ILE B 180 CA CA B 305 1555 1555 2.28 LINK NE2AHIS B 183 ZN ZN B 302 1555 1555 1.99 LINK NE2BHIS B 183 ZN ZN B 302 1555 1555 2.03 LINK O GLY B 190 CA CA B 303 1555 1555 2.35 LINK O GLY B 192 CA CA B 303 1555 1555 2.26 LINK OD1 ASP B 194 CA CA B 303 1555 1555 2.72 LINK ND1 HIS B 196 ZN ZN B 302 1555 1555 2.05 LINK OD2 ASP B 198 CA CA B 305 1555 1555 2.24 LINK O GLU B 199 CA CA B 304 1555 1555 2.32 LINK OE2 GLU B 199 CA CA B 304 1555 1555 2.39 LINK O GLU B 201 CA CA B 304 1555 1555 2.39 LINK OE2 GLU B 201 CA CA B 305 1555 1555 2.36 LINK NE2 HIS B 218 ZN ZN B 301 1555 1555 2.01 LINK NE2 HIS B 222 ZN ZN B 301 1555 1555 2.01 LINK NE2 HIS B 228 ZN ZN B 301 1555 1555 2.03 LINK ZN ZN B 301 O62 0ZD B 306 1555 1555 1.88 LINK CA CA B 303 O HOH B 442 1555 1555 2.50 LINK CA CA B 304 O HOH B 407 1555 1555 2.37 LINK CA CA B 304 O HOH B 408 1555 1555 2.32 CISPEP 1 GLY B 106 PRO B 107 0 7.62 SITE 1 AC1 4 HIS A 218 HIS A 222 HIS A 228 0ZD B 306 SITE 1 AC2 4 HIS A 168 ASP A 170 HIS A 183 HIS A 196 SITE 1 AC3 6 ASP A 158 GLY A 190 GLY A 192 ASP A 194 SITE 2 AC3 6 HOH A 416 HOH A 424 SITE 1 AC4 5 ASP A 124 GLU A 199 GLU A 201 HOH A 404 SITE 2 AC4 5 HOH A 405 SITE 1 AC5 6 ASP A 175 GLY A 176 GLY A 178 ILE A 180 SITE 2 AC5 6 ASP A 198 GLU A 201 SITE 1 AC6 9 VAL A 144 THR A 145 PRO A 146 LYS A 151 SITE 2 AC6 9 ASN A 153 GLN A 259 HOH A 437 HOH A 498 SITE 3 AC6 9 HOH A 538 SITE 1 AC7 6 ASP A 170 HIS A 172 PHE A 185 ILE A 191 SITE 2 AC7 6 SER B 207 GLY B 208 SITE 1 AC8 5 TYR A 132 LYS A 136 PHE A 213 ILE A 245 SITE 2 AC8 5 HOH A 532 SITE 1 AC9 7 VAL A 108 TRP A 109 ARG A 110 GLY A 188 SITE 2 AC9 7 SER A 189 HOH A 490 HOH A 536 SITE 1 BC1 8 PRO A 232 ALA A 234 VAL A 235 LYS A 241 SITE 2 BC1 8 VAL A 243 HOH A 501 HOH A 503 HOH A 568 SITE 1 BC2 4 HIS A 172 ALA A 184 PHE A 185 HOH A 435 SITE 1 BC3 4 HIS B 218 HIS B 222 HIS B 228 0ZD B 306 SITE 1 BC4 4 HIS B 168 ASP B 170 HIS B 183 HIS B 196 SITE 1 BC5 6 ARG A 110 ASP B 158 GLY B 190 GLY B 192 SITE 2 BC5 6 ASP B 194 HOH B 442 SITE 1 BC6 5 ASP B 124 GLU B 199 GLU B 201 HOH B 407 SITE 2 BC6 5 HOH B 408 SITE 1 BC7 6 ASP B 175 GLY B 176 GLY B 178 ILE B 180 SITE 2 BC7 6 ASP B 198 GLU B 201 SITE 1 BC8 38 ILE A 180 LEU A 181 ALA A 182 LEU A 214 SITE 2 BC8 38 THR A 215 HIS A 218 GLU A 219 HIS A 222 SITE 3 BC8 38 HIS A 228 VAL A 235 PHE A 237 PRO A 238 SITE 4 BC8 38 THR A 239 TYR A 240 ZN A 301 HOH A 401 SITE 5 BC8 38 HOH A 433 ILE B 180 LEU B 181 ALA B 182 SITE 6 BC8 38 LEU B 214 THR B 215 HIS B 218 GLU B 219 SITE 7 BC8 38 HIS B 222 HIS B 228 VAL B 235 PHE B 237 SITE 8 BC8 38 PRO B 238 THR B 239 TYR B 240 ZN B 301 SITE 9 BC8 38 GOL B 308 HOH B 438 HOH B 449 HOH B 451 SITE 10 BC8 38 HOH B 472 HOH B 514 SITE 1 BC9 8 MET B 105 GLY B 225 LEU B 226 GLY B 227 SITE 2 BC9 8 GLY B 257 SER B 260 LEU B 261 HOH B 532 SITE 1 CC1 4 SER B 229 SER B 230 PRO B 238 0ZD B 306 SITE 1 CC2 7 ASP B 171 HIS B 172 HOH B 467 HOH B 468 SITE 2 CC2 7 HOH B 550 HOH B 585 HOH B 610 CRYST1 46.910 61.750 112.560 90.00 90.00 90.00 P 21 21 21 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 0.021317 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016194 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008884 0.00000