Header list of 1bm6.pdb file
Complete list - b 16 2 Bytes
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
MODEL 1
Complete list - b 16 2 Bytes