PDB Short entry for 1FLS HEADER HYDROLASE 15-AUG-00 1FLS TITLE SOLUTION STRUCTURE OF THE CATALYTIC FRAGMENT OF HUMAN COLLAGENASE-3 TITLE 2 (MMP-13) COMPLEXED WITH A HYDROXAMIC ACID INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGENASE-3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC FRAGMENT; COMPND 5 SYNONYM: MMP-13; COMPND 6 EC: 3.4.24.-; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: HYDROXAMIC ACID INHIBITOR COMPLEX 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: PPROMMP-13 KEYWDS MATRIX METALLOPROTEINASE, HYDROXAMIC ACID, HUMAN COLLAGENASE-3, MMP- KEYWDS 2 13, HYDROLASE EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR F.J.MOY,P.K.CHANDA,J.M.CHEN,S.COSMI,W.EDRIS,J.I.LEVIN,R.POWERS REVDAT 3 23-FEB-22 1FLS 1 REMARK LINK REVDAT 2 24-FEB-09 1FLS 1 VERSN REVDAT 1 15-AUG-01 1FLS 0 JRNL AUTH F.J.MOY,P.K.CHANDA,J.M.CHEN,S.COSMI,W.EDRIS,J.I.LEVIN, JRNL AUTH 2 R.POWERS JRNL TITL HIGH-RESOLUTION SOLUTION STRUCTURE OF THE CATALYTIC FRAGMENT JRNL TITL 2 OF HUMAN COLLAGENASE-3 (MMP-13) COMPLEXED WITH A HYDROXAMIC JRNL TITL 3 ACID INHIBITOR. JRNL REF J.MOL.BIOL. V. 302 671 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10986126 JRNL DOI 10.1006/JMBI.2000.4082 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.J MOY,P.K.CHANDA,S.COSMI,W.EDRIS,J.I.LEVIN,R.POWERS REMARK 1 TITL 1H, 15N, 13C, AND 13CO ASSIGNMENTS AND SECONDARY STRUCTURE REMARK 1 TITL 2 DETERMINATION OF COLLAGENASE-3 (MMP-13) COMPLEXED WITH A REMARK 1 TITL 3 HYDROXAMIC ACID INHIBITOR REMARK 1 REF J.BIOMOL.NMR V. 17 269 2000 REMARK 1 REFN ISSN 0925-2738 REMARK 1 DOI 10.1023/A:1008305025043 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.0, X-PLOR 3.840 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS BASED ON 3280 REMARK 3 EXPERIMENTAL NMR RESTRAINTS, CONSISTING OF 2415 APPROXIMATE REMARK 3 INTERPROTON DISTANCE RESTRAINTS, 47 DISTANCE RESTRAINTS BETWEEN REMARK 3 MMP-13 AND WAY-151693, 5 INTRAMOLECULAR DISTANCE RESTRAINTS FOR REMARK 3 WAY-151693, 88 DISTANCE RESTRAINTS FOR 44 BACKBONE HYDROGEN REMARK 3 BONDS, 391 TORSION ANGLE RESTRAINTS, 103 3JNHA RESTRAINTS 123 CA REMARK 3 RESTRAINTS AND 108 CB RESTRAINTS.THE STRUCTURE WAS ALSO REFINED REMARK 3 WITH A CONFORMATIONAL DATABASE. REMARK 4 REMARK 4 1FLS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-AUG-00. REMARK 100 THE DEPOSITION ID IS D_1000011695. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 10 MM DEUTERATED TRIS-BASE, 100 REMARK 210 MM NACL, 5 MM CACL2, 0.1 MM REMARK 210 ZNCL2, 2 MM NAN3, 10 MM REMARK 210 DEUTERATED DTT REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM U-15N,13C-LABELED MMP-13 REMARK 210 WITH WAY-151693 IN A 1:1 RATIO, REMARK 210 10MM DEUTERATED TRIS-BASE, 100MM REMARK 210 NACL, 5MM CACL2, 0.1MM ZNCL2, REMARK 210 2MM NAN3, 10MM DEUTERATED DTT IN REMARK 210 100% D2O AT PH 6.5 AND 35C.; 1MM REMARK 210 U-15N,13C-LABELED MMP-13 WITH REMARK 210 WAY-151693 IN A 1:1 RATIO,10MM REMARK 210 DEUTERATED TRIS-BASE, 100MM NACL, REMARK 210 5MM CACL2, 0.1MM ZNCL2, 2MM REMARK 210 NAN3, 10MM DEUTERATED DTT IN 90% REMARK 210 H2O, 10% D2O AT PH 6.5 AND 35C.; REMARK 210 1MM U-15N-LABELED MMP-13 WITH REMARK 210 WAY-151693 IN A 1:1 RATIO,10MM REMARK 210 DEUTERATED TRIS-BASE, 100MM NACL, REMARK 210 5MM CACL2, 0.1MM ZNCL2, 2MM REMARK 210 NAN3, 10MM DEUTERATED DTT IN 90% REMARK 210 H2O, 10% D2O AT PH 6.5 AND 35C. REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; HNHA; 3D_C13- REMARK 210 EDITED/FILTERED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX-2 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 1.7, X-PLOR 3.840, PIPP REMARK 210 4.2.8 REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE AND REMARK 210 ISOTOPE EDITED/FILTERED NMR SPECTROSCOPY. 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 RES C SSSEQI REMARK 465 TYR A 1 REMARK 465 ASN A 2 REMARK 465 VAL A 3 REMARK 465 PHE A 4 REMARK 465 PRO A 5 REMARK 465 ARG A 6 REMARK 465 PRO A 165 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 H ASN A 112 OH TYR A 141 1.46 REMARK 500 OD1 ASP A 132 H GLY A 134 1.54 REMARK 500 O ASP A 99 HE1 TRP A 104 1.54 REMARK 500 O PHE A 39 H SER A 43 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 THR A 23 136.81 50.39 REMARK 500 PRO A 47 17.68 -67.08 REMARK 500 LYS A 67 -84.23 -11.13 REMARK 500 HIS A 69 37.22 -141.78 REMARK 500 PRO A 88 85.39 -59.06 REMARK 500 PRO A 90 -129.16 -65.28 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 167 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 69 NE2 REMARK 620 2 HIS A 84 NE2 117.0 REMARK 620 3 HIS A 97 ND1 90.1 103.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 168 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 76 OD1 REMARK 620 2 GLY A 77 O 79.3 REMARK 620 3 PRO A 78 O 113.4 66.0 REMARK 620 4 SER A 79 O 47.4 80.5 71.3 REMARK 620 5 LEU A 81 O 123.7 136.8 120.5 142.7 REMARK 620 6 LEU A 81 N 76.2 155.2 128.2 85.6 58.8 REMARK 620 7 ASP A 99 OD2 134.1 90.0 101.9 169.9 47.2 104.5 REMARK 620 8 GLU A 102 OE2 161.9 92.5 48.6 115.6 73.1 112.1 61.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 166 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 119 NE2 REMARK 620 2 HIS A 123 NE2 74.2 REMARK 620 3 HIS A 129 NE2 130.9 98.9 REMARK 620 4 WAY A 169 O11 135.0 148.7 71.3 REMARK 620 5 WAY A 169 O13 94.3 100.3 134.3 70.9 REMARK 620 N 1 2 3 4 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 166 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 167 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 168 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE WAY A 169 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FM1 RELATED DB: PDB REMARK 900 ENSEMBLE OF 30 STRUCTURES DBREF 1FLS A 1 165 UNP P45452 MMP13_HUMAN 104 268 SEQRES 1 A 165 TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER LYS MET SEQRES 2 A 165 ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP MET SEQRES 3 A 165 THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS ALA PHE SEQRES 4 A 165 LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE THR ARG SEQRES 5 A 165 LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER PHE GLY SEQRES 6 A 165 ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 A 165 SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO ASN SEQRES 8 A 165 TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU THR TRP SEQRES 9 A 165 THR SER SER SER LYS GLY TYR ASN LEU PHE LEU VAL ALA SEQRES 10 A 165 ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP HIS SER SEQRES 11 A 165 LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR THR TYR SEQRES 12 A 165 THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP ASP VAL SEQRES 13 A 165 GLN GLY ILE GLN SER LEU TYR GLY PRO HET ZN A 166 1 HET ZN A 167 1 HET CA A 168 1 HET WAY A 169 51 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM WAY N-HYDROXY-2-[(4-METHOXY-BENZENESULFONYL)-PYRIDIN-3- HETNAM 2 WAY YLMETHYL-AMINO]-3-METHYL-BENZAMIDE HETSYN WAY WAY-151693 FORMUL 2 ZN 2(ZN 2+) FORMUL 4 CA CA 2+ FORMUL 5 WAY C21 H21 N3 O5 S HELIX 1 1 THR A 27 VAL A 45 1 19 HELIX 2 2 LEU A 113 LEU A 125 1 13 HELIX 3 3 PRO A 152 GLY A 164 1 13 SHEET 1 A 5 ASN A 49 ARG A 52 0 SHEET 2 A 5 ASN A 14 ILE A 19 1 N LEU A 15 O ASN A 49 SHEET 3 A 5 ILE A 60 GLY A 65 1 N ILE A 60 O THR A 16 SHEET 4 A 5 ALA A 96 ASP A 99 1 N ALA A 96 O MET A 61 SHEET 5 A 5 ALA A 83 ALA A 85 -1 O HIS A 84 N HIS A 97 SHEET 1 B 2 TRP A 104 THR A 105 0 SHEET 2 B 2 TYR A 111 ASN A 112 1 O TYR A 111 N THR A 105 LINK NE2 HIS A 69 ZN ZN A 167 1555 1555 2.47 LINK OD1 ASP A 76 CA CA A 168 1555 1555 2.97 LINK O GLY A 77 CA CA A 168 1555 1555 2.89 LINK O PRO A 78 CA CA A 168 1555 1555 2.98 LINK O SER A 79 CA CA A 168 1555 1555 2.91 LINK O LEU A 81 CA CA A 168 1555 1555 2.88 LINK N LEU A 81 CA CA A 168 1555 1555 3.26 LINK NE2 HIS A 84 ZN ZN A 167 1555 1555 2.10 LINK ND1 HIS A 97 ZN ZN A 167 1555 1555 1.89 LINK OD2 ASP A 99 CA CA A 168 1555 1555 2.98 LINK OE2 GLU A 102 CA CA A 168 1555 1555 2.97 LINK NE2 HIS A 119 ZN ZN A 166 1555 1555 2.10 LINK NE2 HIS A 123 ZN ZN A 166 1555 1555 2.17 LINK NE2 HIS A 129 ZN ZN A 166 1555 1555 2.19 LINK ZN ZN A 166 O11 WAY A 169 1555 1555 2.28 LINK ZN ZN A 166 O13 WAY A 169 1555 1555 2.11 SITE 1 AC1 4 HIS A 119 HIS A 123 HIS A 129 WAY A 169 SITE 1 AC2 3 HIS A 69 HIS A 84 HIS A 97 SITE 1 AC3 8 ASP A 76 GLY A 77 PRO A 78 SER A 79 SITE 2 AC3 8 GLY A 80 LEU A 81 ASP A 99 GLU A 102 SITE 1 AC4 11 GLY A 80 LEU A 81 LEU A 82 LEU A 115 SITE 2 AC4 11 VAL A 116 HIS A 119 HIS A 123 HIS A 129 SITE 3 AC4 11 PRO A 139 TYR A 141 ZN A 166 CRYST1 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