HEADER HYDROLASE/HYDROLASE INHIBITOR 11-DEC-00 1HOV
TITLE SOLUTION STRUCTURE OF A CATALYTIC DOMAIN OF MMP-2 COMPLEXED WITH SC-
TITLE 2 74020
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: MATRIX METALLOPROTEINASE-2;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: CATALYTIC DOMAIN;
COMPND 5 EC: 3.4.24.24;
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;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: W3110-II5;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: RECA
KEYWDS ENZYME-INHIBITOR COMPLEX, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 11
AUTHOR Y.FENG,J.J.LIKOS,L.ZHU,H.WOODWARD,G.MUNIE,J.J.MCDONALD,A.M.STEVENS,
AUTHOR 2 C.P.HOWARD,G.A.DE CRESCENZO,D.WELSCH,H.-S.SHIEH,W.C.STALLINGS
REVDAT 4 23-FEB-22 1HOV 1 REMARK LINK
REVDAT 3 24-FEB-09 1HOV 1 VERSN
REVDAT 2 20-DEC-02 1HOV 1 AUTHOR JRNL REMARK
REVDAT 1 12-DEC-01 1HOV 0
JRNL AUTH Y.FENG,J.J.LIKOS,L.ZHU,H.WOODWARD,G.MUNIE,J.J.MCDONALD,
JRNL AUTH 2 A.M.STEVENS,C.P.HOWARD,G.A.DE CRESCENZO,D.WELSCH,H.-S.SHIEH,
JRNL AUTH 3 W.C.STALLINGS
JRNL TITL SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF THE CATALYTIC
JRNL TITL 2 DOMAIN OF MATRIX METALLOPROTEINASE-2 COMPLEXED WITH A
JRNL TITL 3 HYDROXAMIC ACID INHIBITOR
JRNL REF BIOCHIM.BIOPHYS.ACTA V.1598 10 2002
JRNL REFN ISSN 0006-3002
JRNL PMID 12147339
JRNL DOI 10.1016/S0167-4838(02)00307-2
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 TITL 1H, 13C AND 15N RESONANCE ASSIGNMENTS FOR A TRUNCATED AND
REMARK 1 TITL 2 INHIBITED CATALYTIC DOMAIN OF MATRIX METALLOPROTEINASE-2
REMARK 1 REF J.BIOMOL.NMR V. 17 85 2000
REMARK 1 REFN ISSN 0925-2738
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 98.1
REMARK 3 AUTHORS : MSI
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1HOV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-00.
REMARK 100 THE DEPOSITION ID IS D_1000012486.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303
REMARK 210 PH : 7.4
REMARK 210 IONIC STRENGTH : 50
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 0.3-0.4MM U-15N, 13C MMP-2C:
REMARK 210 UNLABELED SC-74020 IN 20MM TRIS-
REMARK 210 D11-HCL, 5MM CACL2, 10UM ZNCL2,
REMARK 210 20UM UNLABELED SC-74020
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA; UNITY
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : VNMR 6.1B, FELIX 97
REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED
REMARK 210 ANNEALING, MOLECULAR DYNAMICS,
REMARK 210 TORSION ANGLE DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 14
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 3
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 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 H ILE A 21 O ILE A 63 1.60
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 TYR A 2 -89.33 53.48
REMARK 500 1 PRO A 6 41.86 -76.03
REMARK 500 1 ARG A 7 -49.23 71.79
REMARK 500 1 LYS A 10 134.05 -30.88
REMARK 500 1 ASP A 12 74.65 -175.87
REMARK 500 1 ASN A 14 -173.81 -53.98
REMARK 500 1 GLN A 15 98.49 47.67
REMARK 500 1 THR A 47 148.15 -178.13
REMARK 500 1 ILE A 54 -168.73 -124.38
REMARK 500 1 HIS A 55 30.23 -176.15
REMARK 500 1 ASP A 56 -32.83 -163.31
REMARK 500 1 GLU A 58 170.42 58.04
REMARK 500 1 ASN A 64 -138.71 178.85
REMARK 500 1 ARG A 67 170.49 60.75
REMARK 500 1 GLU A 69 -96.23 -75.85
REMARK 500 1 HIS A 70 -80.06 78.17
REMARK 500 1 ASP A 72 -90.10 -37.72
REMARK 500 1 TYR A 74 74.32 -179.67
REMARK 500 1 PHE A 76 158.96 50.53
REMARK 500 1 ASP A 77 -29.39 178.56
REMARK 500 1 LYS A 79 -173.56 43.56
REMARK 500 1 ASP A 80 -95.85 -67.15
REMARK 500 1 ALA A 84 -178.07 169.40
REMARK 500 1 HIS A 85 175.86 179.05
REMARK 500 1 ALA A 88 172.78 -48.55
REMARK 500 1 ASP A 101 -78.56 -76.29
REMARK 500 1 ASP A 102 91.16 -66.04
REMARK 500 1 THR A 108 -145.28 -91.89
REMARK 500 1 SER A 109 37.99 -89.90
REMARK 500 1 ALA A 110 -97.30 -64.14
REMARK 500 1 ASN A 111 -46.45 -178.31
REMARK 500 1 SER A 113 110.12 62.20
REMARK 500 1 MET A 126 -96.37 -78.99
REMARK 500 1 GLN A 132 -24.80 82.48
REMARK 500 1 PRO A 140 21.66 -78.97
REMARK 500 1 ASN A 147 20.61 -160.00
REMARK 500 1 PHE A 148 94.05 36.24
REMARK 500 1 TYR A 162 -93.30 -140.11
REMARK 500 2 TYR A 2 -94.28 -58.49
REMARK 500 2 ASN A 3 98.06 60.21
REMARK 500 2 PRO A 6 -161.09 -74.18
REMARK 500 2 ARG A 7 54.44 77.44
REMARK 500 2 LYS A 8 144.59 60.52
REMARK 500 2 LYS A 10 -137.11 -62.34
REMARK 500 2 TRP A 11 44.18 -163.00
REMARK 500 2 ASN A 14 -85.71 -34.18
REMARK 500 2 GLN A 15 106.97 -51.88
REMARK 500 2 TYR A 23 -114.33 -58.07
REMARK 500 2 ASP A 26 81.73 -158.64
REMARK 500 2 THR A 47 149.32 -179.33
REMARK 500
REMARK 500 THIS ENTRY HAS 404 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 168 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 60 O
REMARK 620 2 GLY A 92 O 100.0
REMARK 620 3 GLY A 94 O 82.5 112.6
REMARK 620 4 GLY A 95 N 115.7 132.2 48.0
REMARK 620 5 ASP A 96 N 124.4 125.4 103.8 56.7
REMARK 620 6 ASP A 96 OD1 104.2 68.7 173.0 125.7 70.8
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 165 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 70 NE2
REMARK 620 2 ASP A 72 OD2 84.2
REMARK 620 3 HIS A 85 NE2 134.6 90.5
REMARK 620 4 HIS A 98 ND1 72.8 150.0 92.1
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 167 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 77 OD2
REMARK 620 2 ASP A 77 OD1 45.5
REMARK 620 3 GLY A 78 O 66.6 77.9
REMARK 620 4 LYS A 79 O 108.7 130.4 52.9
REMARK 620 5 ASP A 80 O 82.2 127.3 87.4 62.7
REMARK 620 6 LEU A 82 O 83.3 95.3 143.9 127.0 68.6
REMARK 620 7 ASP A 100 OD1 92.3 67.3 144.5 158.8 119.0 50.5
REMARK 620 8 ASP A 100 OD2 104.0 59.2 109.8 127.8 162.8 95.9 45.6
REMARK 620 9 GLU A 103 OE1 141.9 103.0 88.8 73.5 127.2 127.0 92.2 56.0
REMARK 620 N 1 2 3 4 5 6 7 8
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 120 NE2
REMARK 620 2 HIS A 124 NE2 100.3
REMARK 620 3 HIS A 130 NE2 111.5 71.9
REMARK 620 4 I52 A 800 O26 145.1 106.8 97.8
REMARK 620 5 I52 A 800 O1 85.8 81.2 149.9 77.2
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 165
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 166
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 167
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 168
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE I52 A 800
DBREF 1HOV A 2 148 UNP P08253 MMP2_HUMAN 110 256
SEQRES 1 A 163 MET TYR ASN PHE PHE PRO ARG LYS PRO LYS TRP ASP LYS
SEQRES 2 A 163 ASN GLN ILE THR TYR ARG ILE ILE GLY TYR THR PRO ASP
SEQRES 3 A 163 LEU ASP PRO GLU THR VAL ASP ASP ALA PHE ALA ARG ALA
SEQRES 4 A 163 PHE GLN VAL TRP SER ASP VAL THR PRO LEU ARG PHE SER
SEQRES 5 A 163 ARG ILE HIS ASP GLY GLU ALA ASP ILE MET ILE ASN PHE
SEQRES 6 A 163 GLY ARG TRP GLU HIS GLY ASP GLY TYR PRO PHE ASP GLY
SEQRES 7 A 163 LYS ASP GLY LEU LEU ALA HIS ALA PHE ALA PRO GLY THR
SEQRES 8 A 163 GLY VAL GLY GLY ASP SER HIS PHE ASP ASP ASP GLU LEU
SEQRES 9 A 163 TRP THR ASN THR SER ALA ASN TYR SER LEU PHE LEU VAL
SEQRES 10 A 163 ALA ALA HIS GLU PHE GLY HIS ALA MET GLY LEU GLU HIS
SEQRES 11 A 163 SER GLN ASP PRO GLY ALA LEU MET ALA PRO ILE TYR THR
SEQRES 12 A 163 TYR THR LYS ASN PHE ARG LEU SER GLN ASP ASP ILE LYS
SEQRES 13 A 163 GLY ILE GLN GLU LEU TYR GLY
HET ZN A 165 1
HET ZN A 166 1
HET CA A 167 1
HET CA A 168 1
HET I52 A 800 82
HETNAM ZN ZINC ION
HETNAM CA CALCIUM ION
HETNAM I52 N-{4-[(1-HYDROXYCARBAMOYL-2-METHYL-PROPYL)-(2-
HETNAM 2 I52 MORPHOLIN-4-YL-ETHYL)-SULFAMOYL]-4-PENTYL-BENZAMIDE
HETSYN I52 SC-74020
FORMUL 2 ZN 2(ZN 2+)
FORMUL 4 CA 2(CA 2+)
FORMUL 6 I52 C29 H42 N4 O6 S
HELIX 1 1 ASP A 28 ASP A 45 1 18
HELIX 2 2 SER A 113 ALA A 125 1 13
HELIX 3 3 SER A 151 TYR A 162 1 12
SHEET 1 A 5 PHE A 51 ARG A 53 0
SHEET 2 A 5 ILE A 16 ILE A 20 1 O ILE A 16 N SER A 52
SHEET 3 A 5 ILE A 61 PHE A 65 1 N ILE A 61 O THR A 17
SHEET 4 A 5 SER A 97 PHE A 99 1 N SER A 97 O MET A 62
SHEET 5 A 5 ALA A 84 ALA A 86 -1 O HIS A 85 N HIS A 98
LINK O ASP A 60 CA CA A 168 1555 1555 2.45
LINK NE2 HIS A 70 ZN ZN A 165 1555 1555 2.13
LINK OD2 ASP A 72 ZN ZN A 165 1555 1555 2.29
LINK OD2 ASP A 77 CA CA A 167 1555 1555 2.64
LINK OD1 ASP A 77 CA CA A 167 1555 1555 2.90
LINK O GLY A 78 CA CA A 167 1555 1555 2.59
LINK O LYS A 79 CA CA A 167 1555 1555 2.50
LINK O ASP A 80 CA CA A 167 1555 1555 2.57
LINK O LEU A 82 CA CA A 167 1555 1555 2.57
LINK NE2 HIS A 85 ZN ZN A 165 1555 1555 2.07
LINK O GLY A 92 CA CA A 168 1555 1555 2.47
LINK O GLY A 94 CA CA A 168 1555 1555 2.54
LINK N GLY A 95 CA CA A 168 1555 1555 2.83
LINK N ASP A 96 CA CA A 168 1555 1555 2.84
LINK OD1 ASP A 96 CA CA A 168 1555 1555 2.44
LINK ND1 HIS A 98 ZN ZN A 165 1555 1555 2.26
LINK OD1 ASP A 100 CA CA A 167 1555 1555 2.87
LINK OD2 ASP A 100 CA CA A 167 1555 1555 2.67
LINK OE1 GLU A 103 CA CA A 167 1555 1555 3.13
LINK OE2 GLU A 103 CA CA A 167 1555 1555 2.48
LINK NE2 HIS A 120 ZN ZN A 166 1555 1555 2.16
LINK NE2 HIS A 124 ZN ZN A 166 1555 1555 2.30
LINK NE2 HIS A 130 ZN ZN A 166 1555 1555 2.06
LINK ZN ZN A 166 O26 I52 A 800 1555 1555 2.13
LINK ZN ZN A 166 O1 I52 A 800 1555 1555 2.08
SITE 1 AC1 4 HIS A 70 ASP A 72 HIS A 85 HIS A 98
SITE 1 AC2 4 HIS A 120 HIS A 124 HIS A 130 I52 A 800
SITE 1 AC3 7 ASP A 77 GLY A 78 LYS A 79 ASP A 80
SITE 2 AC3 7 LEU A 82 ASP A 100 GLU A 103
SITE 1 AC4 6 ASP A 60 GLY A 92 VAL A 93 GLY A 94
SITE 2 AC4 6 GLY A 95 ASP A 96
SITE 1 AC5 19 GLY A 81 LEU A 82 LEU A 83 ALA A 84
SITE 2 AC5 19 HIS A 85 HIS A 120 GLU A 121 HIS A 124
SITE 3 AC5 19 HIS A 130 ALA A 136 LEU A 137 ALA A 139
SITE 4 AC5 19 ILE A 141 TYR A 142 THR A 143 THR A 145
SITE 5 AC5 19 PHE A 148 ARG A 149 ZN A 166
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
(ATOM LINES ARE NOT SHOWN.)
END