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