10 20 30 40 50 60 70 80 2JT5 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 20-JUL-07 2JT5
TITLE SOLUTION STRUCTURE OF MATRIX METALLOPROTEINASE 3 (MMP-3) IN TITLE 2 THE PRESENCE OF N-HYDROXY-2-[N-(2-HYDROXYETHYL)BIPHENYL-4- TITLE 3 SULFONAMIDE] HYDROXAMIC ACID (MLC88)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: STROMELYSIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 105-265; COMPND 5 SYNONYM: MATRIX METALLOPROTEINASE-3, MMP-3, TRANSIN-1, SL- COMPND 6 1; COMPND 7 EC: 3.4.24.17; COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MMP3, STMY1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET21A
KEYWDS METALLOPROTEINASE, MMP, CALCIUM, COLLAGEN DEGRADATION, KEYWDS 2 EXTRACELLULAR MATRIX, GLYCOPROTEIN, HYDROLASE, METAL- KEYWDS 3 BINDING, METALLOPROTEASE, POLYMORPHISM, PROTEASE, ZINC, KEYWDS 4 ZYMOGEN
EXPDTA SOLUTION NMR
AUTHOR L.A.ALCARAZ,L.BANCI,I.BERTINI,F.CANTINI,A.DONAIRE,L.GONNELLI
REVDAT 2 24-FEB-09 2JT5 1 VERSN REVDAT 1 19-FEB-08 2JT5 0
JRNL AUTH L.A.ALCARAZ,L.BANCI,I.BERTINI,F.CANTINI,A.DONAIRE, JRNL AUTH 2 L.GONNELLI JRNL TITL MATRIX METALLOPROTEINASE-INHIBITOR INTERACTION: JRNL TITL 2 THE SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF JRNL TITL 3 HUMAN MATRIX METALLOPROTEINASE-3 WITH DIFFERENT JRNL TITL 4 INHIBITORS JRNL REF J.BIOL.INORG.CHEM. V. 12 1197 2007 JRNL REFN ISSN 0949-8257 JRNL PMID 17710450 JRNL DOI 10.1007/S00775-007-0288-9
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH, AUTODOCK 3.0 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR_NIH), MORRIS, GOODSELL, HUEY, LINDSTORM, REMARK 3 HART, KUROWSKI, HALLIDAY, BELEW, OLSON (AUTODOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE DOCKED STRUCTURE WITH AUTODOCK REMARK 3 WAS ENERGY MINIMIZED WITH XPLOR-NIH USING THE EXPERIMENTAL DATA
REMARK 4 REMARK 4 2JT5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-AUG-07. REMARK 100 THE RCSB ID CODE IS RCSB100257.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 8 REMARK 210 IONIC STRENGTH : 300 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-98% 15N] PROTEIN, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC, 3D 1H-15N REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL
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 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 ILE A 89 84.21 -154.88 REMARK 500 PRO A 109 -179.69 -60.41 REMARK 500 GLU A 137 -81.95 -17.25 REMARK 500 PHE A 154 -51.35 -163.46 REMARK 500 PRO A 160 45.44 -76.53 REMARK 500 ALA A 169 -63.54 -143.39 REMARK 500 ILE A 174 23.07 -72.84 REMARK 500 ASP A 181 96.48 -67.12 REMARK 500 ASN A 194 98.32 -62.74 REMARK 500 PHE A 210 -123.76 -102.30 REMARK 500 SER A 212 -163.31 -113.28 REMARK 500 PRO A 221 10.41 -68.81 REMARK 500 TYR A 223 96.76 -69.02 REMARK 500 LEU A 245 -70.57 -73.05 REMARK 500 TYR A 246 79.89 -119.82 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 259 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 139 OE2 REMARK 620 2 ASP A 141 O 101.1 REMARK 620 3 ASN A 175 O 157.6 56.7 REMARK 620 4 ASP A 177 OD1 92.2 79.5 82.1 REMARK 620 5 ASP A 177 OD2 112.4 119.7 80.9 51.7 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 ASP A 153 OD1 88.8 REMARK 620 3 HIS A 166 NE2 102.5 89.3 REMARK 620 4 HIS A 179 ND1 123.4 135.8 109.1 REMARK 620 N 1 2 3 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 OD2 50.4 REMARK 620 3 GLY A 159 O 64.0 93.0 REMARK 620 4 GLY A 161 N 93.3 70.4 62.8 REMARK 620 5 GLY A 161 O 137.4 88.6 115.4 57.3 REMARK 620 6 VAL A 163 O 94.2 82.2 153.9 136.8 90.2 REMARK 620 7 GLU A 184 OE2 122.1 157.5 67.0 90.4 90.9 120.3 REMARK 620 N 1 2 3 4 5 6 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 HIS A 201 NE2 REMARK 620 2 HIS A 205 NE2 89.3 REMARK 620 3 HIS A 211 NE2 112.0 106.4 REMARK 620 4 JT5 A 1 O1 113.2 72.2 134.8 REMARK 620 5 JT5 A 1 O5 87.3 149.0 103.4 80.9 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 256 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 257 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 258 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 259 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE JT5 A 1
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JNP RELATED DB: PDB REMARK 900 RELATED ID: 2JT6 RELATED DB: PDB REMARK 900 RELATED ID: 15395 RELATED DB: BMRB
DBREF 2JT5 A 88 248 UNP P08254 MMP3_HUMAN 105 265
SEQRES 1 A 161 GLY ILE PRO LYS TRP ARG LYS THR HIS LEU THR TYR ARG SEQRES 2 A 161 ILE VAL ASN TYR THR PRO ASP LEU PRO LYS ASP ALA VAL SEQRES 3 A 161 ASP SER ALA VAL GLU LYS ALA LEU LYS VAL TRP GLU GLU SEQRES 4 A 161 VAL THR PRO LEU THR PHE SER ARG LEU TYR GLU GLY GLU SEQRES 5 A 161 ALA ASP ILE MET ILE SER PHE ALA VAL ARG GLU HIS GLY SEQRES 6 A 161 ASP PHE TYR PRO PHE ASP GLY PRO GLY ASN VAL LEU ALA SEQRES 7 A 161 HIS ALA TYR ALA PRO GLY PRO GLY ILE ASN GLY ASP ALA SEQRES 8 A 161 HIS PHE ASP ASP ASP GLU GLN TRP THR LYS ASP THR THR SEQRES 9 A 161 GLY THR ASN LEU PHE LEU VAL ALA ALA HIS GLU ILE GLY SEQRES 10 A 161 HIS SER LEU GLY LEU PHE HIS SER ALA ASN THR GLU ALA SEQRES 11 A 161 LEU MET TYR PRO LEU TYR HIS SER LEU THR ASP LEU THR SEQRES 12 A 161 ARG PHE ARG LEU SER GLN ASP ASP ILE ASN GLY ILE GLN SEQRES 13 A 161 SER LEU TYR GLY PRO
HET ZN A 256 1 HET ZN A 257 1 HET CA A 258 1 HET CA A 259 1 HET JT5 A 1 41
HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM JT5 N~2~-(BIPHENYL-4-YLSULFONYL)-N-HYDROXY-N~2~-(2- HETNAM 2 JT5 HYDROXYETHYL)GLYCINAMIDE
FORMUL 2 ZN 2(ZN 2+) FORMUL 4 CA 2(CA 2+) FORMUL 6 JT5 C16 H18 N2 O5 S
HELIX 1 1 PRO A 90 LYS A 94 5 5 HELIX 2 2 PRO A 109 TRP A 124 1 16 HELIX 3 3 LEU A 195 LEU A 207 1 13 HELIX 4 4 SER A 235 TYR A 246 1 12
SHEET 1 A 5 THR A 131 LEU A 135 0 SHEET 2 A 5 HIS A 96 VAL A 102 1 N TYR A 99 O SER A 133 SHEET 3 A 5 ILE A 142 ALA A 147 1 O ILE A 142 N THR A 98 SHEET 4 A 5 ASP A 177 ASP A 181 1 O PHE A 180 N ALA A 147 SHEET 5 A 5 ALA A 165 TYR A 168 -1 N HIS A 166 O HIS A 179 SHEET 1 B 2 TRP A 186 THR A 187 0 SHEET 2 B 2 THR A 193 ASN A 194 1 O THR A 193 N THR A 187
LINK OE2 GLU A 139 CA CA A 259 1555 1555 2.47 LINK O ASP A 141 CA CA A 259 1555 1555 2.87 LINK NE2 HIS A 151 ZN ZN A 257 1555 1555 2.07 LINK OD1 ASP A 153 ZN ZN A 257 1555 1555 2.17 LINK OD1 ASP A 158 CA CA A 258 1555 1555 2.54 LINK OD2 ASP A 158 CA CA A 258 1555 1555 2.56 LINK O GLY A 159 CA CA A 258 1555 1555 2.53 LINK N GLY A 161 CA CA A 258 1555 1555 2.82 LINK O GLY A 161 CA CA A 258 1555 1555 2.89 LINK O VAL A 163 CA CA A 258 1555 1555 2.34 LINK NE2 HIS A 166 ZN ZN A 257 1555 1555 2.07 LINK O ASN A 175 CA CA A 259 1555 1555 2.52 LINK OD1 ASP A 177 CA CA A 259 1555 1555 2.57 LINK OD2 ASP A 177 CA CA A 259 1555 1555 2.37 LINK ND1 HIS A 179 ZN ZN A 257 1555 1555 2.15 LINK OE2 GLU A 184 CA CA A 258 1555 1555 2.30 LINK NE2 HIS A 201 ZN ZN A 256 1555 1555 2.06 LINK NE2 HIS A 205 ZN ZN A 256 1555 1555 2.07 LINK NE2 HIS A 211 ZN ZN A 256 1555 1555 2.22 LINK ZN ZN A 256 O1 JT5 A 1 1555 1555 2.35 LINK ZN ZN A 256 O5 JT5 A 1 1555 1555 2.07
SITE 1 AC1 4 JT5 A 1 HIS A 201 HIS A 205 HIS A 211 SITE 1 AC2 4 HIS A 151 ASP A 153 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 LEU A 164 GLU A 184 SITE 1 AC4 5 GLU A 139 ASP A 141 GLY A 173 ASN A 175 SITE 2 AC4 5 ASP A 177 SITE 1 AC5 15 ASN A 162 VAL A 163 LEU A 164 ALA A 165 SITE 2 AC5 15 LEU A 197 HIS A 201 GLU A 202 HIS A 205 SITE 3 AC5 15 HIS A 211 LEU A 218 TYR A 220 PRO A 221 SITE 4 AC5 15 LEU A 222 TYR A 223 ZN A 256
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