10 20 30 40 50 60 70 80 1Z3J - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 13-MAR-05 1Z3J
TITLE SOLUTION STRUCTURE OF MMP12 IN THE PRESENCE OF N-ISOBUTYL-N- TITLE 2 4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID (NNGH)
CAVEAT 1Z3J CHIRALITY ERRORS AT CA CENTER OF VAL 108 A
COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACROPHAGE METALLOELASTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 106-263; COMPND 5 SYNONYM: HME, MATRIX METALLOPROTEINASE-12, MMP-12, COMPND 6 MACROPHAGE ELASTASE, ME; COMPND 7 EC: 3.4.24.65; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: 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: PET21 (NOVAGEN)
KEYWDS MACROPHAGE METALLOELASTASE, MMP-12, SOLUTION STRUCTURE, KEYWDS 2 NNGH, ZINC, HYDROLASE
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR I.BERTINI,V.CALDERONE,M.COSENZA,M.FRAGAI,Y.M.LEE,C.LUCHINAT, AUTHOR 2 S.MANGANI,B.TERNI,P.TURANO
REVDAT 2 24-FEB-09 1Z3J 1 VERSN REVDAT 1 19-APR-05 1Z3J 0
JRNL AUTH I.BERTINI,V.CALDERONE,M.COSENZA,M.FRAGAI,Y.M.LEE, JRNL AUTH 2 C.LUCHINAT,S.MANGANI,B.TERNI,P.TURANO JRNL TITL CONFORMATIONAL VARIABILITY OF MATRIX JRNL TITL 2 METALLOPROTEINASES: BEYOND A SINGLE 3D STRUCTURE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 5334 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 15809432 JRNL DOI 10.1073/PNAS.0407106102
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 6.0 REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON, REMARK 3 SEIBEL,SINGH,WEINER,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1Z3J COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-05. REMARK 100 THE RCSB ID CODE IS RCSB032252.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 0.3 M NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.9 MM MMP12 U-15N,13C; 10MM REMARK 210 DEUTERATED TRIS; 5 MM CACL2; REMARK 210 0.1 MM ZNCL2; 0.3 M NACL; 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY, 3D_ REMARK 210 15N-SEPARATED_NOESY, 2D NOESY, REMARK 210 HNHA, ISOTOPE-FILTERED 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ, 800 MHZ, 700 MHZ, REMARK 210 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE, DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.1, XEASY 1.3, DYANA REMARK 210 1.5 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, TORSION ANGLE REMARK 210 DYNAMICS, RESIDUE DIPOLAR REMARK 210 COUPLING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : MINIMIZED AVERAGE STRUCTURE REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING DISTANCE, DIHEDRAL REMARK 210 ANGLE AND H-BOND RESTRAINTS WITH DIPOLAR COUPLING RESTRAINTS
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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 VAL A 108 CB - CA - C ANGL. DEV. = -15.8 DEGREES REMARK 500 LEU A 181 CB - CA - C ANGL. DEV. = 11.5 DEGREES 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 VAL A 108 36.67 136.21 REMARK 500 ARG A 110 -77.04 11.27 REMARK 500 LYS A 111 -69.91 -137.03 REMARK 500 HIS A 112 -66.54 63.85 REMARK 500 ALA A 164 -168.63 -123.30 REMARK 500 ALA A 173 -67.00 64.04 REMARK 500 ASP A 175 20.97 -174.64 REMARK 500 HIS A 228 113.75 7.84 REMARK 500 PHE A 248 85.02 40.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TRP A 109 ARG A 110 116.89 REMARK 500 TYR A 262 GLY A 263 -38.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 110 0.08 SIDE_CHAIN REMARK 500 TYR A 116 0.09 SIDE_CHAIN REMARK 500 ARG A 127 0.09 SIDE_CHAIN REMARK 500 PHE A 149 0.24 SIDE_CHAIN REMARK 500 PHE A 163 0.11 SIDE_CHAIN REMARK 500 ASP A 194 0.07 SIDE_CHAIN REMARK 500 HIS A 196 0.12 SIDE_CHAIN REMARK 500 HIS A 218 0.10 SIDE_CHAIN REMARK 500 PHE A 248 0.13 SIDE_CHAIN REMARK 500 TYR A 262 0.17 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (11X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 VAL A 108 104.9 ALPHA-CARBON 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 266 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 199 OE2 REMARK 620 2 GLU A 199 O 72.8 REMARK 620 3 GLU A 201 O 134.4 67.2 REMARK 620 4 ASP A 124 OD2 130.7 147.2 81.2 REMARK 620 5 ASP A 124 OD1 78.6 137.1 118.0 52.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 267 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 180 O REMARK 620 2 ASP A 175 OD2 70.8 REMARK 620 3 GLY A 178 O 74.9 63.3 REMARK 620 4 GLY A 176 O 165.5 101.8 90.6 REMARK 620 5 GLU A 201 OE2 101.7 142.7 79.4 76.4 REMARK 620 6 ASP A 198 OD1 74.2 94.5 146.6 119.5 119.2 REMARK 620 7 ASP A 198 OD2 115.3 138.2 157.4 78.7 78.7 53.1 REMARK 620 8 ASP A 175 OD1 96.3 26.1 74.6 78.3 143.2 96.4 121.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 268 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 192 O REMARK 620 2 ASP A 194 OD2 116.3 REMARK 620 3 GLY A 190 O 80.3 84.6 REMARK 620 4 ILE A 191 O 58.0 58.7 69.8 REMARK 620 5 ASP A 194 OD1 107.8 51.0 134.4 77.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 264 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NGH A 269 O4 REMARK 620 2 HIS A 228 NE2 172.0 REMARK 620 3 HIS A 222 NE2 97.0 80.1 REMARK 620 4 HIS A 218 NE2 77.4 109.1 79.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 265 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 170 OD1 REMARK 620 2 ASP A 170 OD2 59.5 REMARK 620 3 HIS A 183 NE2 114.8 89.6 REMARK 620 4 HIS A 196 ND1 158.7 118.5 85.8 REMARK 620 5 HIS A 168 NE2 84.1 143.6 107.2 95.3 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 264 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 265 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 266 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 267 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 268 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NGH A 269
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YCM RELATED DB: PDB REMARK 900 SAME STRUCTURE, 20 MODELS ENSEMBLE
DBREF 1Z3J A 106 263 UNP P39900 MMP12_HUMAN 106 263
SEQADV 1Z3J MET A 105 UNP P39900 INITIATING METHIONINE SEQADV 1Z3J ASP A 171 UNP P39900 PHE 171 ENGINEERED
SEQRES 1 A 159 MET GLY PRO VAL TRP ARG LYS HIS TYR ILE THR TYR ARG SEQRES 2 A 159 ILE ASN ASN TYR THR PRO ASP MET ASN ARG GLU ASP VAL SEQRES 3 A 159 ASP TYR ALA ILE ARG LYS ALA PHE GLN VAL TRP SER ASN SEQRES 4 A 159 VAL THR PRO LEU LYS PHE SER LYS ILE ASN THR GLY MET SEQRES 5 A 159 ALA ASP ILE LEU VAL VAL PHE ALA ARG GLY ALA HIS GLY SEQRES 6 A 159 ASP ASP HIS ALA PHE ASP GLY LYS GLY GLY ILE LEU ALA SEQRES 7 A 159 HIS ALA PHE GLY PRO GLY SER GLY ILE GLY GLY ASP ALA SEQRES 8 A 159 HIS PHE ASP GLU ASP GLU PHE TRP THR THR HIS SER GLY SEQRES 9 A 159 GLY THR ASN LEU PHE LEU THR ALA VAL HIS GLU ILE GLY SEQRES 10 A 159 HIS SER LEU GLY LEU GLY HIS SER SER ASP PRO LYS ALA SEQRES 11 A 159 VAL MET PHE PRO THR TYR LYS TYR VAL ASP ILE ASN THR SEQRES 12 A 159 PHE ARG LEU SER ALA ASP ASP ILE ARG GLY ILE GLN SER SEQRES 13 A 159 LEU TYR GLY
HET ZN A 264 1 HET ZN A 265 1 HET CA A 266 1 HET CA A 267 1 HET CA A 268 1 HET NGH A 269 40
HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM NGH N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HETNAM 2 NGH HYDROXAMIC ACID
FORMUL 2 ZN 2(ZN 2+) FORMUL 4 CA 3(CA 2+) FORMUL 7 NGH C13 H20 N2 O5 S
HELIX 1 1 ASN A 126 THR A 145 1 20 HELIX 2 2 LEU A 212 GLY A 225 1 14 HELIX 3 3 SER A 251 SER A 260 1 10
SHEET 1 A 5 LYS A 148 LYS A 151 0 SHEET 2 A 5 TYR A 113 ILE A 118 1 N ILE A 114 O SER A 150 SHEET 3 A 5 ILE A 159 PHE A 163 1 O VAL A 161 N ARG A 117 SHEET 4 A 5 ALA A 195 PHE A 197 1 O PHE A 197 N VAL A 162 SHEET 5 A 5 ALA A 182 ALA A 184 -1 N HIS A 183 O HIS A 196 SHEET 1 B 2 TRP A 203 THR A 204 0 SHEET 2 B 2 THR A 210 ASN A 211 1 O THR A 210 N THR A 204
LINK CA CA A 266 OE2 GLU A 199 1555 1555 2.26 LINK CA CA A 266 O GLU A 199 1555 1555 2.26 LINK CA CA A 266 O GLU A 201 1555 1555 2.49 LINK CA CA A 266 OD2 ASP A 124 1555 1555 2.27 LINK CA CA A 267 O ILE A 180 1555 1555 2.35 LINK CA CA A 267 OD2 ASP A 175 1555 1555 3.99 LINK CA CA A 267 O GLY A 178 1555 1555 2.38 LINK CA CA A 267 O GLY A 176 1555 1555 2.38 LINK CA CA A 267 OE2 GLU A 201 1555 1555 2.24 LINK CA CA A 267 OD1 ASP A 198 1555 1555 2.31 LINK CA CA A 267 OD2 ASP A 198 1555 1555 2.42 LINK CA CA A 268 O GLY A 192 1555 1555 2.40 LINK CA CA A 268 OD2 ASP A 194 1555 1555 2.59 LINK CA CA A 268 O GLY A 190 1555 1555 2.62 LINK ZN ZN A 264 O4 NGH A 269 1555 1555 2.11 LINK ZN ZN A 264 NE2 HIS A 228 1555 1555 2.13 LINK ZN ZN A 264 NE2 HIS A 222 1555 1555 2.08 LINK ZN ZN A 264 NE2 HIS A 218 1555 1555 2.08 LINK ZN ZN A 265 OD1 ASP A 170 1555 1555 2.06 LINK ZN ZN A 265 OD2 ASP A 170 1555 1555 2.20 LINK ZN ZN A 265 NE2 HIS A 183 1555 1555 2.21 LINK ZN ZN A 265 ND1 HIS A 196 1555 1555 2.26 LINK ZN ZN A 265 NE2 HIS A 168 1555 1555 2.32 LINK CA CA A 266 OD1 ASP A 124 1555 1555 2.53 LINK CA CA A 267 OD1 ASP A 175 1555 1555 2.23 LINK CA CA A 268 O ILE A 191 1555 1555 2.99 LINK CA CA A 268 OD1 ASP A 194 1555 1555 2.26
CISPEP 1 MET A 105 GLY A 106 0 5.82 CISPEP 2 PRO A 107 VAL A 108 0 -5.88
SITE 1 AC1 4 HIS A 218 HIS A 222 HIS A 228 NGH A 269 SITE 1 AC2 4 HIS A 168 ASP A 170 HIS A 183 HIS A 196 SITE 1 AC3 4 THR A 122 ASP A 124 GLU A 199 GLU A 201 SITE 1 AC4 6 ASP A 175 GLY A 176 GLY A 178 ILE A 180 SITE 2 AC4 6 ASP A 198 GLU A 201 SITE 1 AC5 4 GLY A 190 ILE A 191 GLY A 192 ASP A 194 SITE 1 AC6 13 GLY A 179 ILE A 180 LEU A 181 ALA A 182 SITE 2 AC6 13 LEU A 214 THR A 215 HIS A 218 GLU A 219 SITE 3 AC6 13 HIS A 222 PRO A 238 THR A 239 TYR A 240 SITE 4 AC6 13 ZN A 264
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