HEADER HYDROLASE/HYDROLASE INHIBITOR 14-APR-00 1EUB TITLE SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN COLLAGENASE-3 TITLE 2 (MMP-13) COMPLEXED TO A POTENT NON-PEPTIDIC SULFONAMIDE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGENASE 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: MATRIX METALLOPROTEINASE-13, MMP-13; COMPND 6 EC: 3.4.24.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET3D-CD-CLN3 KEYWDS ALPHA HELIX, BETA SHEET, PROTEIN-INHIBITOR COMPLEX, HYDROLASE- KEYWDS 2 HYDROLASE INHIBITOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR X.ZHANG,N.C.GONNELLA,J.KOEHN,N.PATHAK,V.GANU,R.MELTON,D.PARKER, AUTHOR 2 S.I.HU,K.Y.NAM REVDAT 5 22-MAY-24 1EUB 1 REMARK REVDAT 4 16-FEB-22 1EUB 1 REMARK LINK REVDAT 3 24-FEB-09 1EUB 1 VERSN REVDAT 2 01-APR-03 1EUB 1 JRNL REVDAT 1 14-APR-01 1EUB 0 JRNL AUTH X.ZHANG,N.C.GONNELLA,J.KOEHN,N.PATHAK,V.GANU,R.MELTON, JRNL AUTH 2 D.PARKER,S.I.HU,K.Y.NAM JRNL TITL SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JRNL TITL 2 COLLAGENASE-3 (MMP-13) COMPLEXED TO A POTENT NON-PEPTIDIC JRNL TITL 3 SULFONAMIDE INHIBITOR: BINDING COMPARISON WITH STROMELYSIN-1 JRNL TITL 4 AND COLLAGENASE-1. JRNL REF J.MOL.BIOL. V. 301 513 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10926524 JRNL DOI 10.1006/JMBI.2000.3988 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 98.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EUB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAY-00. REMARK 100 THE DEPOSITION ID IS D_1000010898. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310.00 REMARK 210 PH : 6.80 REMARK 210 IONIC STRENGTH : 100 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM COLLAGENASE-3 15N, 13C, REMARK 210 20 MM TRIS D11, 20 MM CACL2, REMARK 210 0.02% NAN3, 5 MM DTT, 100 MM REMARK 210 NACL, 0.1 MM ZNCL, REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 3D 15N EDITED NOESY; 2D REMARK 210 15N HSQC; 2D 13C HMQC; 3D REMARK 210 CBCA(CO)NH; 3D HBHA(CO)NH; 3D REMARK 210 HNCACB; 3D HNCO; 15N FILTERED REMARK 210 NOESY; 2D 13C FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 97, NMRCOMPASS 2.5, REMARK 210 INSIGHT II 98, QUANTA 97 REMARK 210 METHOD USED : SIMULATED ANNEALING AND ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM, REMARK 210 STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND ENERGY, REMARK 210 TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING 2D AND 3D REMARK 210 HETERONUCLEAR NMR TECHNIQUES 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 O ASP A 202 H GLU A 205 1.48 REMARK 500 H THR A 130 OE1 GLU A 133 1.59 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 VAL A 106 -90.84 -156.50 REMARK 500 1 THR A 110 -60.65 -171.63 REMARK 500 1 LEU A 111 30.50 39.41 REMARK 500 1 TRP A 113 -65.58 -153.52 REMARK 500 1 SER A 114 59.97 -105.02 REMARK 500 1 LYS A 115 53.45 -154.57 REMARK 500 1 VAL A 123 42.17 -162.82 REMARK 500 1 ASN A 124 -81.67 -40.63 REMARK 500 1 PRO A 127 -86.67 -75.85 REMARK 500 1 LYS A 139 -71.67 -66.07 REMARK 500 1 ILE A 160 70.93 -119.85 REMARK 500 1 LYS A 170 93.79 1.08 REMARK 500 1 GLU A 171 23.53 -146.16 REMARK 500 1 HIS A 172 -67.15 -96.89 REMARK 500 1 ASP A 174 -82.62 -121.51 REMARK 500 1 ASP A 179 83.00 179.56 REMARK 500 1 SER A 182 165.57 -41.06 REMARK 500 1 LEU A 184 89.28 179.78 REMARK 500 1 PRO A 191 74.50 -67.53 REMARK 500 1 PRO A 193 -159.99 -74.37 REMARK 500 1 ASP A 202 92.78 -48.78 REMARK 500 1 ASP A 203 -27.98 -36.33 REMARK 500 1 LYS A 212 106.26 -170.00 REMARK 500 1 LEU A 218 -72.10 -78.50 REMARK 500 1 SER A 227 -39.64 -38.74 REMARK 500 1 LEU A 230 -170.49 -177.68 REMARK 500 1 SER A 233 60.43 179.92 REMARK 500 1 LYS A 234 26.40 -148.12 REMARK 500 1 MET A 240 -34.00 -140.42 REMARK 500 1 PHE A 241 170.54 -58.11 REMARK 500 1 THR A 245 -72.54 4.25 REMARK 500 1 LYS A 249 51.63 -148.73 REMARK 500 1 HIS A 251 -64.20 -173.65 REMARK 500 1 PHE A 252 177.02 179.90 REMARK 500 1 MET A 253 48.94 -75.33 REMARK 500 1 VAL A 259 -76.09 -62.26 REMARK 500 1 GLU A 271 29.32 46.46 REMARK 500 2 VAL A 106 -89.43 -135.34 REMARK 500 2 PRO A 108 -158.67 -75.32 REMARK 500 2 ARG A 109 82.65 70.94 REMARK 500 2 THR A 110 -64.72 -149.15 REMARK 500 2 LEU A 111 40.08 36.30 REMARK 500 2 TRP A 113 -70.32 -151.64 REMARK 500 2 SER A 114 77.74 -102.40 REMARK 500 2 LYS A 115 51.19 -169.31 REMARK 500 2 TYR A 120 -169.24 -174.43 REMARK 500 2 VAL A 123 56.86 -149.90 REMARK 500 2 ASN A 124 -82.29 -44.34 REMARK 500 2 TYR A 125 -173.95 -178.69 REMARK 500 2 PRO A 127 -86.11 -78.26 REMARK 500 REMARK 500 THIS ENTRY HAS 780 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 CA A 277 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 162 O REMARK 620 2 ASN A 194 O 163.2 REMARK 620 3 TYR A 195 N 148.5 40.5 REMARK 620 4 GLY A 196 O 55.7 141.1 107.6 REMARK 620 5 GLY A 196 N 104.5 89.0 49.5 59.2 REMARK 620 6 ASP A 198 OD1 100.3 91.9 92.5 62.8 79.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 275 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 172 NE2 REMARK 620 2 HIS A 187 NE2 107.8 REMARK 620 3 HIS A 200 ND1 122.9 113.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 278 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 179 OD1 REMARK 620 2 GLY A 180 O 87.2 REMARK 620 3 SER A 182 O 107.0 113.4 REMARK 620 4 LEU A 184 O 105.2 137.6 101.6 REMARK 620 5 ASP A 202 OD2 54.4 106.4 135.2 56.6 REMARK 620 6 GLU A 205 OE2 163.0 77.4 73.5 91.2 136.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 276 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 222 NE2 REMARK 620 2 HIS A 226 NE2 118.5 REMARK 620 3 HIS A 232 NE2 163.2 68.9 REMARK 620 4 MET A 240 O 86.8 127.2 77.3 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 275 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 276 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 277 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 278 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 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 456C RELATED DB: PDB REMARK 900 456C CONTAINS AN X-RAY STRUCTURE OF THE SAME PROTEIN COMPLEXED TO A REMARK 900 SULFONE HYDROXAMIC ACID REMARK 900 RELATED ID: 830C RELATED DB: PDB REMARK 900 830C CONTAINS AN X-RAY STRUCTURE OF THE SAME PROTEIN COMPLEXED TO A REMARK 900 SULFONE HYDROXAMIC ACID DBREF 1EUB A 104 274 UNP P45452 COGZ_HUMAN 104 274 SEQRES 1 A 171 TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER LYS MET SEQRES 2 A 171 ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP MET SEQRES 3 A 171 THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS ALA PHE SEQRES 4 A 171 LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE THR ARG SEQRES 5 A 171 LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER PHE GLY SEQRES 6 A 171 ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 A 171 SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO ASN SEQRES 8 A 171 TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU THR TRP SEQRES 9 A 171 THR SER SER SER LYS GLY TYR ASN LEU PHE LEU VAL ALA SEQRES 10 A 171 ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP HIS SER SEQRES 11 A 171 LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR THR TYR SEQRES 12 A 171 THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP ASP VAL SEQRES 13 A 171 GLN GLY ILE GLN SER LEU TYR GLY PRO GLY ASP GLU ASP SEQRES 14 A 171 PRO ASN HET ZN A 275 1 HET ZN A 276 1 HET CA A 277 1 HET CA A 278 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 THR A 130 THR A 149 1 20 HELIX 2 2 PHE A 217 LEU A 228 1 12 HELIX 3 3 PRO A 255 TYR A 266 1 12 SHEET 1 A 4 ASN A 152 THR A 154 0 SHEET 2 A 4 ASN A 117 VAL A 123 1 N LEU A 118 O ASN A 152 SHEET 3 A 4 ILE A 163 GLY A 168 1 N ILE A 163 O THR A 119 SHEET 4 A 4 ASP A 198 ASP A 202 1 O ALA A 199 N SER A 166 LINK NA HAV A 1 CB 3MP A 2 1555 1555 1.48 LINK NA HAV A 1 S MSB A 3 1555 1555 1.64 LINK O ASP A 162 CA CA A 277 1555 1555 2.57 LINK NE2 HIS A 172 ZN ZN A 275 1555 1555 2.17 LINK OD1 ASP A 179 CA CA A 278 1555 1555 2.57 LINK O GLY A 180 CA CA A 278 1555 1555 2.59 LINK O SER A 182 CA CA A 278 1555 1555 2.58 LINK O LEU A 184 CA CA A 278 1555 1555 2.59 LINK NE2 HIS A 187 ZN ZN A 275 1555 1555 2.08 LINK O ASN A 194 CA CA A 277 1555 1555 2.58 LINK N TYR A 195 CA CA A 277 1555 1555 3.38 LINK O GLY A 196 CA CA A 277 1555 1555 2.48 LINK N GLY A 196 CA CA A 277 1555 1555 2.91 LINK OD1 ASP A 198 CA CA A 277 1555 1555 2.57 LINK ND1 HIS A 200 ZN ZN A 275 1555 1555 2.08 LINK OD2 ASP A 202 CA CA A 278 1555 1555 2.46 LINK OE2 GLU A 205 CA CA A 278 1555 1555 2.52 LINK NE2 HIS A 222 ZN ZN A 276 1555 1555 2.17 LINK NE2 HIS A 226 ZN ZN A 276 1555 1555 2.25 LINK NE2 HIS A 232 ZN ZN A 276 1555 1555 2.20 LINK O MET A 240 ZN ZN A 276 1555 1555 1.97 SITE 1 AC1 3 HIS A 172 HIS A 187 HIS A 200 SITE 1 AC2 5 HAV A 1 HIS A 222 HIS A 226 HIS A 232 SITE 2 AC2 5 MET A 240 SITE 1 AC3 5 ASP A 162 ASN A 194 TYR A 195 GLY A 196 SITE 2 AC3 5 ASP A 198 SITE 1 AC4 7 ASP A 179 GLY A 180 PRO A 181 SER A 182 SITE 2 AC4 7 LEU A 184 ASP A 202 GLU A 205 SITE 1 AC5 9 3MP A 2 MSB A 3 LEU A 184 ALA A 186 SITE 2 AC5 9 HIS A 222 GLU A 223 HIS A 226 HIS A 232 SITE 3 AC5 9 ZN A 276 SITE 1 AC6 4 HAV A 1 MSB A 3 GLY A 183 PRO A 242 SITE 1 AC7 10 HAV A 1 3MP A 2 LEU A 185 ALA A 186 SITE 2 AC7 10 LEU A 218 HIS A 222 PHE A 241 PRO A 242 SITE 3 AC7 10 ILE A 243 TYR A 244 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 MODEL 1