PDB Short entry for 1BM6 HEADER METALLOPROTEASE 29-JUL-98 1BM6 TITLE SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN STROMELYSIN-1 TITLE 2 COMPLEXED TO A POTENT NON-PEPTIDIC INHIBITOR, NMR, 20 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: STROMELYSIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MMP-3; COMPND 5 EC: 3.4.24.17; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PRO-SFSTR; SOURCE 9 EXPRESSION_SYSTEM_GENE: HUMAN STROMELYSIN-1 KEYWDS HYDROLASE, METALLOPROTEASE, METZINCINS EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.LI,X.ZHANG,R.MELTON,V.GANU,N.C.GONNELLA REVDAT 3 16-FEB-22 1BM6 1 REMARK LINK REVDAT 2 24-FEB-09 1BM6 1 VERSN REVDAT 1 29-JUL-99 1BM6 0 JRNL AUTH Y.C.LI,X.ZHANG,R.MELTON,V.GANU,N.C.GONNELLA JRNL TITL SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JRNL TITL 2 STROMELYSIN-1 COMPLEXED TO A POTENT, NONPEPTIDIC INHIBITOR. JRNL REF BIOCHEMISTRY V. 37 14048 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9760240 JRNL DOI 10.1021/BI981328W REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.R.GOOLEY,J.F.O'CONNELL,A.I.MARCY,G.C.CUCA,S.P.SALOWE, REMARK 1 AUTH 2 B.L.BUSH,J.D.HERMES,C.K.ESSER,W.K.HAGMANN,J.P.SPRINGER, REMARK 1 AUTH 3 B.A.JOHNSON REMARK 1 TITL THE NMR STRUCTURE OF THE INHIBITED CATALYTIC DOMAIN OF HUMAN REMARK 1 TITL 2 STROMELYSIN-1 REMARK 1 REF NAT.STRUCT.BIOL. V. 1 111 1994 REMARK 1 REFN ISSN 1072-8368 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 1BM6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171904. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H; 15N HSQC; 13C; HMQC; 3D REMARK 210 CBCA(CO)NH; 3D HNCA; 3D HNHA; 3D REMARK 210 HCCH-TOCSY; 13C-FILTERED COSY; REMARK 210 15N FILTERED NOESY; 3D 15N REMARK 210 EDITED NOESY; 3D 13C EDITED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : BRUKER XWINNMR XWINNMR, MSI REMARK 210 NMRCOMPASS NMRCOMPASS, FELIX, REMARK 210 NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION, REMARK 210 ENERGY MINIMIZATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY USING 13C,15N STROMELYSIN CATALYTIC DOMAIN. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 OG1 THR A 187 H GLY A 192 1.47 REMARK 500 O ILE A 174 H GLY A 176 1.48 REMARK 500 H TYR A 136 OE1 GLU A 137 1.50 REMARK 500 O GLY A 204 H LEU A 209 1.54 REMARK 500 H VAL A 102 O ILE A 144 1.54 REMARK 500 O LEU A 222 H HIS A 224 1.54 REMARK 500 O THR A 98 H ASP A 141 1.57 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 1 ARG A 84 -162.18 -173.57 REMARK 500 1 LYS A 91 -75.55 -59.22 REMARK 500 1 LYS A 94 170.76 -43.58 REMARK 500 1 TYR A 104 167.54 178.09 REMARK 500 1 LEU A 135 -163.73 -164.81 REMARK 500 1 TYR A 136 28.31 -160.95 REMARK 500 1 GLU A 139 121.43 178.83 REMARK 500 1 ALA A 140 -151.46 -77.58 REMARK 500 1 MET A 143 98.24 -65.13 REMARK 500 1 ARG A 149 83.79 -55.97 REMARK 500 1 GLU A 150 32.07 179.85 REMARK 500 1 ASP A 153 24.96 -159.84 REMARK 500 1 TYR A 155 69.60 1.54 REMARK 500 1 PHE A 157 -169.42 -78.33 REMARK 500 1 ASP A 158 58.92 178.64 REMARK 500 1 VAL A 163 84.38 -55.54 REMARK 500 1 HIS A 166 167.48 178.94 REMARK 500 1 TYR A 168 -166.51 -110.30 REMARK 500 1 PRO A 172 -93.76 -72.60 REMARK 500 1 ASN A 175 62.43 -63.18 REMARK 500 1 ASP A 177 118.33 -163.27 REMARK 500 1 GLU A 184 -98.52 -112.54 REMARK 500 1 GLN A 185 165.28 178.53 REMARK 500 1 ASP A 189 -149.14 -83.28 REMARK 500 1 THR A 193 -98.16 -122.67 REMARK 500 1 ASN A 194 68.14 -160.45 REMARK 500 1 LEU A 195 -97.08 -29.73 REMARK 500 1 LEU A 209 -162.25 -169.02 REMARK 500 1 PHE A 210 -72.64 -99.61 REMARK 500 1 HIS A 211 101.79 -161.13 REMARK 500 1 ALA A 213 86.12 -61.90 REMARK 500 1 ALA A 217 -170.16 -63.72 REMARK 500 1 LEU A 222 -59.21 -21.47 REMARK 500 1 TYR A 223 56.77 -68.00 REMARK 500 1 HIS A 224 -124.13 179.16 REMARK 500 1 LEU A 226 43.78 179.38 REMARK 500 1 ASP A 228 -25.36 179.62 REMARK 500 1 LEU A 229 -97.79 -25.74 REMARK 500 1 PHE A 232 101.66 1.04 REMARK 500 1 ARG A 233 174.62 178.34 REMARK 500 1 SER A 235 -169.88 -101.87 REMARK 500 1 TYR A 246 -115.69 -100.32 REMARK 500 1 ASP A 251 -64.98 -161.66 REMARK 500 1 SER A 252 105.28 -44.68 REMARK 500 2 ARG A 84 -148.57 -78.53 REMARK 500 2 THR A 85 179.97 -50.00 REMARK 500 2 PRO A 90 -167.99 -72.21 REMARK 500 2 LYS A 91 -93.41 -89.45 REMARK 500 2 LYS A 94 -165.81 -55.17 REMARK 500 2 ILE A 101 61.02 -100.22 REMARK 500 REMARK 500 THIS ENTRY HAS 961 RAMACHANDRAN OUTLIERS. 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 256 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HAV A 1 O1 REMARK 620 2 HAV A 1 O 63.0 REMARK 620 3 HIS A 201 NE2 68.3 58.3 REMARK 620 4 HIS A 205 NE2 67.5 126.9 117.9 REMARK 620 5 HIS A 211 NE2 152.4 117.9 137.7 97.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 259 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 141 O REMARK 620 2 GLY A 173 O 166.3 REMARK 620 3 ASN A 175 O 60.8 127.3 REMARK 620 4 GLY A 176 O 50.5 116.0 90.7 REMARK 620 5 ASP A 177 OD1 106.4 60.2 121.9 55.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 257 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 151 NE2 REMARK 620 2 HIS A 166 NE2 131.0 REMARK 620 3 HIS A 179 ND1 82.7 141.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 258 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 158 OD1 REMARK 620 2 ASP A 158 O 53.2 REMARK 620 3 GLY A 159 O 117.9 69.7 REMARK 620 4 GLY A 159 N 81.3 46.6 75.9 REMARK 620 5 GLY A 161 O 82.2 93.3 78.4 138.0 REMARK 620 6 VAL A 163 O 74.9 125.6 164.0 117.3 94.9 REMARK 620 7 ASP A 181 OD2 97.9 94.0 109.3 50.6 170.9 76.4 REMARK 620 8 GLU A 184 OE2 171.0 118.1 53.3 93.9 96.5 114.2 84.7 REMARK 620 N 1 2 3 4 5 6 7 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 256 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 257 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 258 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HAV A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3MP A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MSB A 3 DBREF 1BM6 A 83 255 UNP P08254 MM03_HUMAN 100 272 SEQRES 1 A 173 PHE ARG THR PHE PRO GLY ILE PRO LYS TRP ARG LYS THR SEQRES 2 A 173 HIS LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP LEU SEQRES 3 A 173 PRO LYS ASP ALA VAL ASP SER ALA VAL GLU LYS ALA LEU SEQRES 4 A 173 LYS VAL TRP GLU GLU VAL THR PRO LEU THR PHE SER ARG SEQRES 5 A 173 LEU TYR GLU GLY GLU ALA ASP ILE MET ILE SER PHE ALA SEQRES 6 A 173 VAL ARG GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 A 173 GLY ASN VAL LEU ALA HIS ALA TYR ALA PRO GLY PRO GLY SEQRES 8 A 173 ILE ASN GLY ASP ALA HIS PHE ASP ASP ASP GLU GLN TRP SEQRES 9 A 173 THR LYS ASP THR THR GLY THR ASN LEU PHE LEU VAL ALA SEQRES 10 A 173 ALA HIS GLU ILE GLY HIS SER LEU GLY LEU PHE HIS SER SEQRES 11 A 173 ALA ASN THR GLU ALA LEU MET TYR PRO LEU TYR HIS SER SEQRES 12 A 173 LEU THR ASP LEU THR ARG PHE ARG LEU SER GLN ASP ASP SEQRES 13 A 173 ILE ASN GLY ILE GLN SER LEU TYR GLY PRO PRO PRO ASP SEQRES 14 A 173 SER PRO GLU THR HET ZN A 256 1 HET ZN A 257 1 HET CA A 258 1 HET CA A 259 1 HET HAV A 1 19 HET 3MP A 2 13 HET MSB A 3 18 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM HAV HYDROXYAMINOVALINE HETNAM 3MP 3-METHYLPYRIDINE HETNAM MSB 1-METHYLOXY-4-SULFONE-BENZENE FORMUL 2 ZN 2(ZN 2+) FORMUL 4 CA 2(CA 2+) FORMUL 6 HAV C5 H12 N2 O2 FORMUL 7 3MP C6 H7 N FORMUL 8 MSB C7 H8 O3 S HELIX 1 1 LYS A 110 VAL A 127 1 18 HELIX 2 2 LEU A 195 LEU A 207 1 13 HELIX 3 3 GLN A 236 LEU A 245 1 10 SHEET 1 A 5 THR A 131 LEU A 135 0 SHEET 2 A 5 HIS A 96 VAL A 102 1 N LEU A 97 O THR A 131 SHEET 3 A 5 ILE A 142 ALA A 147 1 N ILE A 142 O ARG A 100 SHEET 4 A 5 ALA A 178 ASP A 181 1 N PHE A 180 O SER A 145 SHEET 5 A 5 ALA A 165 ALA A 167 -1 N HIS A 166 O HIS A 179 LINK NA HAV A 1 CB 3MP A 2 1555 1555 1.49 LINK NA HAV A 1 S MSB A 3 1555 1555 1.63 LINK O1 HAV A 1 ZN ZN A 256 1555 1555 2.28 LINK O HAV A 1 ZN ZN A 256 1555 1555 2.73 LINK O ASP A 141 CA CA A 259 1555 1555 2.69 LINK NE2 HIS A 151 ZN ZN A 257 1555 1555 2.20 LINK OD1 ASP A 158 CA CA A 258 1555 1555 2.62 LINK O ASP A 158 CA CA A 258 1555 1555 2.50 LINK O GLY A 159 CA CA A 258 1555 1555 2.58 LINK N GLY A 159 CA CA A 258 1555 1555 2.98 LINK O GLY A 161 CA CA A 258 1555 1555 2.59 LINK O VAL A 163 CA CA A 258 1555 1555 2.58 LINK NE2 HIS A 166 ZN ZN A 257 1555 1555 2.31 LINK O GLY A 173 CA CA A 259 1555 1555 2.67 LINK O ASN A 175 CA CA A 259 1555 1555 2.56 LINK O GLY A 176 CA CA A 259 1555 1555 2.43 LINK OD1 ASP A 177 CA CA A 259 1555 1555 2.52 LINK ND1 HIS A 179 ZN ZN A 257 1555 1555 2.19 LINK OD2 ASP A 181 CA CA A 258 1555 1555 2.59 LINK OE2 GLU A 184 CA CA A 258 1555 1555 2.62 LINK NE2 HIS A 201 ZN ZN A 256 1555 1555 2.19 LINK NE2 HIS A 205 ZN ZN A 256 1555 1555 2.17 LINK NE2 HIS A 211 ZN ZN A 256 1555 1555 2.18 SITE 1 AC1 5 HAV A 1 HIS A 201 HIS A 205 HIS A 211 SITE 2 AC1 5 MET A 219 SITE 1 AC2 4 HIS A 151 PHE A 157 HIS A 166 HIS A 179 SITE 1 AC3 6 ASP A 158 GLY A 159 GLY A 161 VAL A 163 SITE 2 AC3 6 ASP A 181 GLU A 184 SITE 1 AC4 6 ASP A 141 GLY A 173 ILE A 174 ASN A 175 SITE 2 AC4 6 GLY A 176 ASP A 177 SITE 1 AC5 7 3MP A 2 MSB A 3 VAL A 163 ALA A 165 SITE 2 AC5 7 HIS A 201 HIS A 205 ZN A 256 SITE 1 AC6 3 HAV A 1 MSB A 3 ASN A 162 SITE 1 AC7 14 HAV A 1 3MP A 2 ASN A 162 VAL A 163 SITE 2 AC7 14 LEU A 164 ALA A 165 LEU A 197 VAL A 198 SITE 3 AC7 14 HIS A 201 LEU A 218 MET A 219 TYR A 220 SITE 4 AC7 14 PRO A 221 LEU A 222 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000