HEADER HYDROLASE 04-FEB-16 5I0L TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-12 IN COMPLEX WITH A TITLE 2 SELECTIVE SUGAR-CONJUGATED ARYLSULFONAMIDE CARBOXYLATE WATER-SOLUBLE TITLE 3 INHIBITOR (DC27). COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACROPHAGE METALLOELASTASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 106-263; COMPND 5 SYNONYM: MME,MACROPHAGE ELASTASE,HME,MATRIX METALLOPROTEINASE-12,MMP- COMPND 6 12; COMPND 7 EC: 3.4.24.65; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 OTHER_DETAILS: CATALYTIC DOMAIN OF MMP-12 WITH F171D MUTATION. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: MACROPHAGE; SOURCE 6 GENE: MMP12, HME; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: STAR KEYWDS INHIBITOR, COMPLEX, GLYCOCONJUGATE, METALLOPROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR E.A.STURA,L.ROSALIA,D.CUFFARO,L.TEPSHI,L.CICCONE,A.ROSSELLO REVDAT 5 10-JAN-24 5I0L 1 LINK REVDAT 4 16-NOV-16 5I0L 1 REVDAT 3 17-AUG-16 5I0L 1 JRNL REVDAT 2 13-JUL-16 5I0L 1 JRNL REVDAT 1 06-JUL-16 5I0L 0 JRNL AUTH E.NUTI,D.CUFFARO,F.D'ANDREA,L.ROSALIA,L.TEPSHI,M.FABBI, JRNL AUTH 2 G.CARBOTTI,S.FERRINI,S.SANTAMARIA,C.CAMODECA,L.CICCONE, JRNL AUTH 3 E.ORLANDINI,S.NENCETTI,E.A.STURA,V.DIVE,A.ROSSELLO JRNL TITL SUGAR-BASED ARYLSULFONAMIDE CARBOXYLATES AS SELECTIVE AND JRNL TITL 2 WATER-SOLUBLE MATRIX METALLOPROTEINASE-12 INHIBITORS. JRNL REF CHEMMEDCHEM V. 11 1626 2016 JRNL REFN ESSN 1860-7187 JRNL PMID 27356908 JRNL DOI 10.1002/CMDC.201600235 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 11075 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 555 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 44.2312 - 3.8885 0.99 2668 141 0.1718 0.2296 REMARK 3 2 3.8885 - 3.0867 1.00 2656 140 0.1476 0.2334 REMARK 3 3 3.0867 - 2.6965 0.99 2621 138 0.1718 0.2706 REMARK 3 4 2.6965 - 2.4500 0.99 2575 136 0.2490 0.3420 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.91 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 : 0.015 2766 REMARK 3 ANGLE : 1.754 3757 REMARK 3 CHIRALITY : 0.123 381 REMARK 3 PLANARITY : 0.009 494 REMARK 3 DIHEDRAL : 18.480 975 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 10.3639 15.2171 14.5706 REMARK 3 T TENSOR REMARK 3 T11: 0.0620 T22: 0.0598 REMARK 3 T33: 0.0583 T12: -0.0370 REMARK 3 T13: -0.0006 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 0.0141 L22: 0.0200 REMARK 3 L33: 0.0121 L12: -0.0063 REMARK 3 L13: 0.0098 L23: -0.0004 REMARK 3 S TENSOR REMARK 3 S11: -0.0214 S12: -0.0337 S13: 0.0021 REMARK 3 S21: -0.0135 S22: 0.0692 S23: 0.0284 REMARK 3 S31: 0.0018 S32: 0.0018 S33: -0.0000 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 5I0L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218045. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-15 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 : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.965 REMARK 200 MONOCHROMATOR : SINGLE SILICON (111) 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11195 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.140 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : 0.09300 REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.23 REMARK 200 R MERGE FOR SHELL (I) : 0.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.230 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 4H84 REMARK 200 REMARK 200 REMARK: THIN PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN-INHIBITOR COMPLEX: HMMP12 REMARK 280 0.631 MILLI-M + 0.010 M ACETOHYDROXAMIC ACID + 0.005 M INHIBITOR REMARK 280 DC27, 10% DMSO. PRECIPITANT: 34% PEG 4K, 1.5 M IMIDAZOLE REMARK 280 PIPERIDINE, PH 8.5, DIOXANE 25% CRYOPROTECTANT: 40% CRYOMIX: REMARK 280 (12.5 % DIETHYLENE GLYCOL + 12.5 % GLYCEROL + 12.5 % 1,2- REMARK 280 PROPANEDIOL + 12.5 % 2,3-BUTANEDIOL + 25 % DMSO + 30 % 1,4- REMARK 280 DIOXANE), 25% MPEG 6K, 0.1 M AAB (NA ACETATE, ADA, BICINE: 10% REMARK 280 ACID/90% BASIC), PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 31.43000 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 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 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 105 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 O HOH A 449 O HOH A 521 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 498 O HOH B 502 2646 2.07 REMARK 500 O HOH A 417 O HOH B 541 2646 2.08 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 110 53.06 -101.66 REMARK 500 LYS A 111 149.03 -174.28 REMARK 500 PRO A 146 21.21 -78.33 REMARK 500 HIS A 206 -130.83 -123.34 REMARK 500 HIS B 206 -107.47 -122.04 REMARK 500 ASP B 244 108.09 -55.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU A 128 -14.03 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 = 6.17 ANGSTROMS REMARK 525 HOH B 551 DISTANCE = 7.62 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 305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 124 OD1 REMARK 620 2 ASP A 124 OD2 50.5 REMARK 620 3 GLU A 199 O 151.6 139.5 REMARK 620 4 GLU A 199 OE2 77.1 94.1 75.7 REMARK 620 5 GLU A 201 O 129.3 79.7 73.2 121.3 REMARK 620 6 HOH A 462 O 81.5 130.5 88.2 85.0 140.9 REMARK 620 7 HOH A 522 O 93.2 104.7 105.0 146.1 90.2 61.2 REMARK 620 N 1 2 3 4 5 6 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 158 O REMARK 620 2 GLY A 190 O 161.3 REMARK 620 3 GLY A 192 O 95.6 93.6 REMARK 620 4 ASP A 194 OD1 91.6 104.7 90.4 REMARK 620 5 HOH A 422 O 80.0 86.5 75.7 162.8 REMARK 620 6 HOH A 450 O 96.4 74.7 168.0 90.0 105.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 168 NE2 REMARK 620 2 ASP A 170 OD2 125.0 REMARK 620 3 HIS A 183 NE2 108.8 96.5 REMARK 620 4 HIS A 196 ND1 119.7 97.9 105.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 306 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 175 OD1 REMARK 620 2 GLY A 176 O 80.6 REMARK 620 3 GLY A 178 O 83.8 84.0 REMARK 620 4 ILE A 180 O 91.6 171.7 92.6 REMARK 620 5 ASP A 198 OD2 92.8 92.5 175.4 90.5 REMARK 620 6 GLU A 201 OE2 174.9 98.6 91.1 89.0 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 218 NE2 REMARK 620 2 HIS A 222 NE2 98.4 REMARK 620 3 HIS A 228 NE2 126.8 102.0 REMARK 620 4 H27 A 301 O98 119.1 120.1 91.2 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 124 OD1 REMARK 620 2 ASP B 124 OD2 47.3 REMARK 620 3 GLU B 199 O 165.9 146.7 REMARK 620 4 GLU B 199 OE2 102.3 85.7 83.5 REMARK 620 5 GLU B 201 O 104.8 79.0 81.6 124.7 REMARK 620 6 HOH B 463 O 66.8 103.4 101.7 149.8 85.5 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 158 O REMARK 620 2 GLY B 190 O 164.0 REMARK 620 3 GLY B 192 O 102.6 89.5 REMARK 620 4 ASP B 194 OD1 88.0 101.7 94.7 REMARK 620 5 HOH B 417 O 86.2 79.6 163.5 99.6 REMARK 620 6 HOH B 430 O 92.5 79.3 79.2 173.9 86.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 168 NE2 REMARK 620 2 ASP B 170 OD2 114.2 REMARK 620 3 HIS B 183 NE2 110.4 113.7 REMARK 620 4 HIS B 196 ND1 112.8 97.2 107.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 306 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 175 OD1 REMARK 620 2 GLY B 176 O 89.2 REMARK 620 3 GLY B 178 O 86.6 81.5 REMARK 620 4 ILE B 180 O 87.6 174.2 93.5 REMARK 620 5 ASP B 198 OD2 101.0 92.2 170.1 93.1 REMARK 620 6 GLU B 201 OE2 173.7 88.1 87.4 94.6 84.7 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 218 NE2 REMARK 620 2 HIS B 222 NE2 104.3 REMARK 620 3 HIS B 228 NE2 115.6 105.5 REMARK 620 4 H27 B 301 OZ2 90.0 142.7 98.6 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 H27 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 ZN A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGO A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue H27 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 309 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4H84 RELATED DB: PDB REMARK 900 SAME PROTEIN. THE INHIBITOR IS AN GLYCOCONJUGATE OF THE INHIBITOR REMARK 900 IN ENTRY 4H84. REMARK 900 RELATED ID: 4H30 RELATED DB: PDB REMARK 900 SAME PROTEIN. THE GLYCOCONJUGATE INHIBITOR IN THIS STRUCTURE SHOULD REMARK 900 BE COMPARED WITH THE DIMERIC LIGAND IN ENTRY 4H30. DBREF 5I0L A 106 263 UNP P39900 MMP12_HUMAN 106 263 DBREF 5I0L B 106 263 UNP P39900 MMP12_HUMAN 106 263 SEQADV 5I0L MET A 105 UNP P39900 INITIATING METHIONINE SEQADV 5I0L ASP A 171 UNP P39900 PHE 171 ENGINEERED MUTATION SEQADV 5I0L MET B 105 UNP P39900 INITIATING METHIONINE SEQADV 5I0L 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 H27 A 301 52 HET ZN A 302 1 HET ZN A 303 1 HET CA A 304 1 HET CA A 305 1 HET CA A 306 1 HET PGO A 307 5 HET EDO A 308 4 HET PEG A 309 7 HET H27 B 301 52 HET ZN B 302 1 HET ZN B 303 1 HET CA B 304 1 HET CA B 305 1 HET CA B 306 1 HET EDO B 307 4 HET EDO B 308 4 HET DMS B 309 4 HETNAM H27 (2R)-2-[{(E)-2-[({(2R,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5- HETNAM 2 H27 BIS(ACETYLOXY)-6-[(ACETYLOXY)METHYL]TETRAHYDRO-2H- HETNAM 3 H27 PYRAN-2-YL}CARBAMOTHIOYL)AMINO]ETHENYL}(BIPHENYL-4- HETNAM 4 H27 YLSULFONYL)AMINO]-3-METHYLBUTANOIC ACID HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM PGO S-1,2-PROPANEDIOL HETNAM EDO 1,2-ETHANEDIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM DMS DIMETHYL SULFOXIDE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 H27 2(C34 H42 N4 O12 S2) FORMUL 4 ZN 4(ZN 2+) FORMUL 6 CA 6(CA 2+) FORMUL 9 PGO C3 H8 O2 FORMUL 10 EDO 3(C2 H6 O2) FORMUL 11 PEG C4 H10 O3 FORMUL 20 DMS C2 H6 O S FORMUL 21 HOH *303(H2 O) HELIX 1 AA1 ASN A 126 ASN A 143 1 18 HELIX 2 AA2 LEU A 212 LEU A 224 1 13 HELIX 3 AA3 ASP A 244 PHE A 248 5 5 HELIX 4 AA4 SER A 251 GLY A 263 1 13 HELIX 5 AA5 ASN B 126 ASN B 143 1 18 HELIX 6 AA6 LEU B 212 GLY B 225 1 14 HELIX 7 AA7 SER B 251 GLY B 263 1 13 SHEET 1 AA1 5 LYS A 148 LYS A 151 0 SHEET 2 AA1 5 TYR A 113 ILE A 118 1 N TYR A 116 O SER A 150 SHEET 3 AA1 5 ILE A 159 ALA A 164 1 O ILE A 159 N THR A 115 SHEET 4 AA1 5 ALA A 195 ASP A 198 1 O PHE A 197 N VAL A 162 SHEET 5 AA1 5 ALA A 182 ALA A 184 -1 N HIS A 183 O HIS A 196 SHEET 1 AA2 2 TRP A 203 THR A 204 0 SHEET 2 AA2 2 THR A 210 ASN A 211 1 O THR A 210 N THR A 204 SHEET 1 AA3 5 LYS B 148 LYS B 151 0 SHEET 2 AA3 5 TYR B 113 ILE B 118 1 N ILE B 114 O LYS B 148 SHEET 3 AA3 5 ILE B 159 ALA B 164 1 O VAL B 161 N ARG B 117 SHEET 4 AA3 5 ALA B 195 ASP B 198 1 O PHE B 197 N VAL B 162 SHEET 5 AA3 5 ALA B 182 ALA B 184 -1 N HIS B 183 O HIS B 196 SHEET 1 AA4 2 TRP B 203 THR B 204 0 SHEET 2 AA4 2 THR B 210 ASN B 211 1 O THR B 210 N THR B 204 LINK OD1 ASP A 124 CA CA A 305 1555 1555 2.74 LINK OD2 ASP A 124 CA CA A 305 1555 1555 2.36 LINK O ASP A 158 CA CA A 304 1555 1555 2.25 LINK NE2 HIS A 168 ZN ZN A 303 1555 1555 1.97 LINK OD2 ASP A 170 ZN ZN A 303 1555 1555 1.80 LINK OD1 ASP A 175 CA CA A 306 1555 1555 2.40 LINK O GLY A 176 CA CA A 306 1555 1555 2.27 LINK O GLY A 178 CA CA A 306 1555 1555 2.39 LINK O ILE A 180 CA CA A 306 1555 1555 2.16 LINK NE2 HIS A 183 ZN ZN A 303 1555 1555 2.15 LINK O GLY A 190 CA CA A 304 1555 1555 2.37 LINK O GLY A 192 CA CA A 304 1555 1555 2.33 LINK OD1 ASP A 194 CA CA A 304 1555 1555 2.39 LINK ND1 HIS A 196 ZN ZN A 303 1555 1555 2.19 LINK OD2 ASP A 198 CA CA A 306 1555 1555 2.37 LINK O GLU A 199 CA CA A 305 1555 1555 2.28 LINK OE2 GLU A 199 CA CA A 305 1555 1555 2.42 LINK O GLU A 201 CA CA A 305 1555 1555 2.49 LINK OE2 GLU A 201 CA CA A 306 1555 1555 2.17 LINK NE2 HIS A 218 ZN ZN A 302 1555 1555 2.19 LINK NE2 HIS A 222 ZN ZN A 302 1555 1555 2.09 LINK NE2 HIS A 228 ZN ZN A 302 1555 1555 2.70 LINK O98 H27 A 301 ZN ZN A 302 1555 1555 1.75 LINK CA CA A 304 O HOH A 422 1555 1555 2.33 LINK CA CA A 304 O HOH A 450 1555 1555 2.30 LINK CA CA A 305 O HOH A 462 1555 1555 2.52 LINK CA CA A 305 O HOH A 522 1555 1555 2.88 LINK OD1 ASP B 124 CA CA B 305 1555 1555 2.92 LINK OD2 ASP B 124 CA CA B 305 1555 1555 2.33 LINK O ASP B 158 CA CA B 304 1555 1555 2.22 LINK NE2 HIS B 168 ZN ZN B 303 1555 1555 2.08 LINK OD2 ASP B 170 ZN ZN B 303 1555 1555 1.75 LINK OD1 ASP B 175 CA CA B 306 1555 1555 2.16 LINK O GLY B 176 CA CA B 306 1555 1555 2.23 LINK O GLY B 178 CA CA B 306 1555 1555 2.37 LINK O ILE B 180 CA CA B 306 1555 1555 2.20 LINK NE2 HIS B 183 ZN ZN B 303 1555 1555 2.10 LINK O GLY B 190 CA CA B 304 1555 1555 2.35 LINK O GLY B 192 CA CA B 304 1555 1555 2.37 LINK OD1 ASP B 194 CA CA B 304 1555 1555 2.45 LINK ND1 HIS B 196 ZN ZN B 303 1555 1555 2.22 LINK OD2 ASP B 198 CA CA B 306 1555 1555 2.28 LINK O GLU B 199 CA CA B 305 1555 1555 2.18 LINK OE2 GLU B 199 CA CA B 305 1555 1555 2.33 LINK O GLU B 201 CA CA B 305 1555 1555 2.47 LINK OE2 GLU B 201 CA CA B 306 1555 1555 2.19 LINK NE2 HIS B 218 ZN ZN B 302 1555 1555 2.15 LINK NE2 HIS B 222 ZN ZN B 302 1555 1555 1.93 LINK NE2 HIS B 228 ZN ZN B 302 1555 1555 2.24 LINK OZ2 H27 B 301 ZN ZN B 302 1555 1555 1.99 LINK CA CA B 304 O HOH B 417 1555 1555 2.38 LINK CA CA B 304 O HOH B 430 1555 1555 2.39 LINK CA CA B 305 O HOH B 463 1555 1555 2.21 SITE 1 AC1 15 ILE A 180 LEU A 181 ALA A 182 HIS A 183 SITE 2 AC1 15 LEU A 214 HIS A 218 GLU A 219 HIS A 222 SITE 3 AC1 15 HIS A 228 VAL A 235 PHE A 237 PRO A 238 SITE 4 AC1 15 TYR A 240 ZN A 302 HOH A 434 SITE 1 AC2 4 HIS A 218 HIS A 222 HIS A 228 H27 A 301 SITE 1 AC3 4 HIS A 168 ASP A 170 HIS A 183 HIS A 196 SITE 1 AC4 6 ASP A 158 GLY A 190 GLY A 192 ASP A 194 SITE 2 AC4 6 HOH A 422 HOH A 450 SITE 1 AC5 5 ASP A 124 GLU A 199 GLU A 201 HOH A 462 SITE 2 AC5 5 HOH A 522 SITE 1 AC6 6 ASP A 175 GLY A 176 GLY A 178 ILE A 180 SITE 2 AC6 6 ASP A 198 GLU A 201 SITE 1 AC7 2 GLY A 227 ASP A 253 SITE 1 AC8 6 TRP A 109 HIS A 112 LYS A 177 ASP A 200 SITE 2 AC8 6 LEU A 261 HOH A 522 SITE 1 AC9 2 ASP A 253 ARG A 256 SITE 1 AD1 22 PRO A 232 LYS A 233 LYS A 241 HOH A 409 SITE 2 AD1 22 GLY B 179 ILE B 180 LEU B 181 ALA B 182 SITE 3 AD1 22 LEU B 214 THR B 215 HIS B 218 GLU B 219 SITE 4 AD1 22 HIS B 222 HIS B 228 VAL B 235 PHE B 237 SITE 5 AD1 22 PRO B 238 THR B 239 ZN B 302 EDO B 308 SITE 6 AD1 22 DMS B 309 HOH B 401 SITE 1 AD2 4 HIS B 218 HIS B 222 HIS B 228 H27 B 301 SITE 1 AD3 4 HIS B 168 ASP B 170 HIS B 183 HIS B 196 SITE 1 AD4 6 ASP B 158 GLY B 190 GLY B 192 ASP B 194 SITE 2 AD4 6 HOH B 417 HOH B 430 SITE 1 AD5 4 ASP B 124 GLU B 199 GLU B 201 HOH B 463 SITE 1 AD6 6 ASP B 175 GLY B 176 GLY B 178 ILE B 180 SITE 2 AD6 6 ASP B 198 GLU B 201 SITE 1 AD7 3 VAL B 108 TRP B 109 ARG B 110 SITE 1 AD8 4 ILE B 180 H27 B 301 HOH B 404 HOH B 464 SITE 1 AD9 7 GLY B 179 LEU B 181 THR B 239 TYR B 240 SITE 2 AD9 7 H27 B 301 HOH B 457 HOH B 479 CRYST1 39.090 62.860 63.750 90.00 102.54 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 0.025582 0.000000 0.005690 0.00000 SCALE2 0.000000 0.015908 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016070 0.00000