PDB Short entry for 6TT8 HEADER METAL BINDING PROTEIN 25-DEC-19 6TT8 TITLE HADDOCK MODEL OF NDM-1/MORIN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLO BETA LACTAMASE NDM-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: METALLO BETA-LACTAMASE,METALLO-BETA-LACTAMASE,NDM-1,NDM COMPND 5 CARBAPENEMASE,NDM-1 METALLO-BETA-LACTAMASE,NDM1 METALLO-BETA- COMPND 6 LACTAMASE,NEW DELHI METALLO CARBAPENEMASE-1,NEW DELHI METALLO-BETA- COMPND 7 LACTAMSE 1,SUBCLASS B1 METALLO-BETA-LACTAMASE NDM-1; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: BLANDM-1, BLA NDM-1, BLANDM-1_1, BLANDM-1_2, BLANDM-1_3, SOURCE 5 BLANDM1, NDM-1, BANRA_05884, C3483_29595, C7V41_28630, D647_P47098, SOURCE 6 EC13450_007, FAQ72_26810, FAQ97_27095, FAS39_27275, NCTC13443_00040, SOURCE 7 P2146_00143, PCRE380_21, PMK1_NDM00067, PMK1_NDM00076, SOURCE 8 PMK1_NDM00085, PN11X00042NDM_090, PNDM-SX04_5, PNDM10469_138, SOURCE 9 SAMEA3531848_05178, TR3_031, TR4_031; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, INHIBITOR, MORIN, NEW-DELHI METALLO-BETA-LACTAMASE-1, KEYWDS 2 HADDOCK, ANTIMICROBIAL RESISTANCE, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 56 AUTHOR G.RIVIERE,S.OUESLATI,M.GAYRAL,J.B.CRECHET,N.NHIRI,E.JACQUET, AUTHOR 2 J.C.CINTRAT,F.GIRAUD,C.VAN HEIJENOORT,E.LESCOP,S.PETHE,B.I.IORGA, AUTHOR 3 T.NAAS,E.GUITTET,N.MORELLET REVDAT 2 17-MAR-21 6TT8 1 JRNL REVDAT 1 13-JAN-21 6TT8 0 JRNL AUTH G.RIVIERE,S.OUESLATI,M.GAYRAL,J.B.CRECHET,N.NHIRI,E.JACQUET, JRNL AUTH 2 J.C.CINTRAT,F.GIRAUD,C.VAN HEIJENOORT,E.LESCOP,S.PETHE, JRNL AUTH 3 B.I.IORGA,T.NAAS,E.GUITTET,N.MORELLET JRNL TITL NMR CHARACTERIZATION OF THE INFLUENCE OF ZINC(II) IONS ON JRNL TITL 2 THE STRUCTURAL AND DYNAMIC BEHAVIOR OF THE NEW DELHI JRNL TITL 3 METALLO-BETA-LACTAMASE-1 AND ON THE BINDING WITH FLAVONOLS JRNL TITL 4 AS INHIBITORS. JRNL REF ACS OMEGA V. 5 10466 2020 JRNL REFN ESSN 2470-1343 JRNL PMID 32426604 JRNL DOI 10.1021/ACSOMEGA.0C00590 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK REMARK 3 AUTHORS : BONVIN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6TT8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292105975. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 320 UM [U-13C; U-15N] NDM-1, REMARK 210 1280 UM MORIN, 0.1 MM BIS-TRIS, REMARK 210 150 MM SODIUM CHLORIDE, 2.5 % REMARK 210 DMSO, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCA; 3D HNCACB; 3D HN(CO)CA; 3D REMARK 210 HN(COCA)CB REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CCPNMR ANALYSIS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 2800 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 56 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 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 ZN ZN A 302 OAD MRI A 303 1.46 REMARK 500 OD2 ASP A 124 ZN ZN A 302 1.65 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 PHE A 70 -51.84 -123.69 REMARK 500 1 ASP A 90 158.48 71.25 REMARK 500 1 LYS A 125 -30.25 -132.16 REMARK 500 1 MET A 126 53.60 -116.28 REMARK 500 2 PRO A 68 127.86 -37.35 REMARK 500 2 ASP A 90 143.51 72.30 REMARK 500 2 THR A 91 -161.32 -100.85 REMARK 500 2 ASP A 202 38.81 -86.54 REMARK 500 2 ASP A 254 -163.58 -102.03 REMARK 500 3 PHE A 70 59.21 -141.11 REMARK 500 3 ASP A 90 151.28 72.78 REMARK 500 3 THR A 91 -163.86 -108.26 REMARK 500 3 THR A 226 43.37 -82.09 REMARK 500 3 GLU A 227 -44.06 -142.86 REMARK 500 4 PRO A 68 103.63 -38.51 REMARK 500 4 ASP A 90 153.28 71.25 REMARK 500 4 THR A 91 -166.62 -110.41 REMARK 500 4 THR A 226 31.04 -81.75 REMARK 500 4 GLU A 227 -51.99 -144.00 REMARK 500 4 PRO A 253 99.06 -60.97 REMARK 500 4 SER A 255 -167.69 -101.75 REMARK 500 5 PRO A 68 101.92 -44.92 REMARK 500 5 ASP A 90 147.29 71.95 REMARK 500 5 LEU A 221 52.59 -118.62 REMARK 500 6 ASP A 90 149.03 71.68 REMARK 500 6 ASP A 202 40.80 -91.20 REMARK 500 7 PRO A 68 103.34 -41.69 REMARK 500 7 ASP A 90 145.73 71.84 REMARK 500 7 THR A 91 -167.89 -102.93 REMARK 500 8 ASP A 90 158.22 68.93 REMARK 500 8 GLU A 108 -64.11 -91.58 REMARK 500 8 ALA A 114 -64.66 -98.87 REMARK 500 8 THR A 226 43.06 -81.04 REMARK 500 8 GLU A 227 -57.65 -146.12 REMARK 500 9 PRO A 68 107.54 -32.65 REMARK 500 9 ASP A 90 144.13 71.67 REMARK 500 9 THR A 91 -167.11 -103.45 REMARK 500 10 PHE A 70 -66.59 -150.46 REMARK 500 10 ASP A 90 165.81 70.29 REMARK 500 10 LYS A 125 -31.33 -143.17 REMARK 500 10 THR A 226 26.54 -77.45 REMARK 500 10 GLU A 227 -51.41 -137.94 REMARK 500 10 ASP A 254 -168.02 -109.91 REMARK 500 10 SER A 255 -167.28 -100.06 REMARK 500 11 PHE A 70 -67.44 -140.73 REMARK 500 11 ASP A 90 150.33 72.04 REMARK 500 11 THR A 91 -167.05 -103.81 REMARK 500 12 PHE A 70 -50.19 -158.87 REMARK 500 12 ASP A 90 151.58 73.61 REMARK 500 12 THR A 91 -165.30 -107.71 REMARK 500 REMARK 500 THIS ENTRY HAS 237 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 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HIS A 122 ND1 121.4 REMARK 620 3 HIS A 189 NE2 112.9 108.5 REMARK 620 4 MRI A 303 OAC 134.1 86.9 86.3 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MRI A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34471 RELATED DB: BMRB REMARK 900 HADDOCK MODEL OF NDM-1/MORIN COMPLEX DBREF 6TT8 A 43 269 UNP E9NWK5 E9NWK5_KLEPN 43 269 SEQRES 1 A 227 ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG GLN LEU ALA SEQRES 2 A 227 PRO ASN VAL TRP GLN HIS THR SER TYR LEU ASP MET PRO SEQRES 3 A 227 GLY PHE GLY ALA VAL ALA SER ASN GLY LEU ILE VAL ARG SEQRES 4 A 227 ASP GLY GLY ARG VAL LEU VAL VAL ASP THR ALA TRP THR SEQRES 5 A 227 ASP ASP GLN THR ALA GLN ILE LEU ASN TRP ILE LYS GLN SEQRES 6 A 227 GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL VAL THR HIS SEQRES 7 A 227 ALA HIS GLN ASP LYS MET GLY GLY MET ASP ALA LEU HIS SEQRES 8 A 227 ALA ALA GLY ILE ALA THR TYR ALA ASN ALA LEU SER ASN SEQRES 9 A 227 GLN LEU ALA PRO GLN GLU GLY MET VAL ALA ALA GLN HIS SEQRES 10 A 227 SER LEU THR PHE ALA ALA ASN GLY TRP VAL GLU PRO ALA SEQRES 11 A 227 THR ALA PRO ASN PHE GLY PRO LEU LYS VAL PHE TYR PRO SEQRES 12 A 227 GLY PRO GLY HIS THR SER ASP ASN ILE THR VAL GLY ILE SEQRES 13 A 227 ASP GLY THR ASP ILE ALA PHE GLY GLY CYS LEU ILE LYS SEQRES 14 A 227 ASP SER LYS ALA LYS SER LEU GLY ASN LEU GLY ASP ALA SEQRES 15 A 227 ASP THR GLU HIS TYR ALA ALA SER ALA ARG ALA PHE GLY SEQRES 16 A 227 ALA ALA PHE PRO LYS ALA SER MET ILE VAL MET SER HIS SEQRES 17 A 227 SER ALA PRO ASP SER ARG ALA ALA ILE THR HIS THR ALA SEQRES 18 A 227 ARG MET ALA ASP LYS LEU HET ZN A 301 1 HET ZN A 302 1 HET MRI A 303 27 HETNAM ZN ZINC ION HETNAM MRI 2-[2,4-BIS(OXIDANYL)PHENYL]-3,5,7-TRIS(OXIDANYL) HETNAM 2 MRI CHROMEN-4-ONE HETSYN MRI MORIN FORMUL 2 ZN 2(ZN 2+) FORMUL 4 MRI C15 H10 O7 HELIX 1 AA1 THR A 94 GLU A 108 1 15 HELIX 2 AA2 GLY A 128 GLY A 136 1 9 HELIX 3 AA3 ALA A 143 GLY A 153 1 11 HELIX 4 AA4 HIS A 228 PHE A 240 1 13 HELIX 5 AA5 ARG A 256 ASP A 267 1 12 SHEET 1 AA1 8 GLN A 44 PHE A 46 0 SHEET 2 AA1 8 LEU A 49 ALA A 55 -1 O PHE A 51 N GLN A 44 SHEET 3 AA1 8 VAL A 58 MET A 67 -1 O GLN A 60 N ARG A 52 SHEET 4 AA1 8 GLY A 71 ASP A 82 -1 O GLY A 71 N MET A 67 SHEET 5 AA1 8 ARG A 85 VAL A 89 -1 O LEU A 87 N VAL A 80 SHEET 6 AA1 8 VAL A 113 VAL A 117 1 O ALA A 114 N VAL A 86 SHEET 7 AA1 8 ALA A 138 ASN A 142 1 O TYR A 140 N ALA A 116 SHEET 8 AA1 8 HIS A 159 LEU A 161 1 O LEU A 161 N ALA A 141 SHEET 1 AA2 4 LEU A 180 PHE A 183 0 SHEET 2 AA2 4 THR A 195 ILE A 198 -1 O THR A 195 N PHE A 183 SHEET 3 AA2 4 ILE A 203 GLY A 207 -1 O PHE A 205 N VAL A 196 SHEET 4 AA2 4 MET A 245 MET A 248 1 O VAL A 247 N GLY A 206 LINK NE2 HIS A 120 ZN ZN A 301 1555 1555 1.91 LINK ND1 HIS A 122 ZN ZN A 301 1555 1555 1.83 LINK NE2 HIS A 189 ZN ZN A 301 1555 1555 1.96 LINK NE2 HIS A 250 ZN ZN A 302 1555 1555 1.87 LINK ZN ZN A 301 OAC MRI A 303 1555 1555 2.05 SITE 1 AC1 5 HIS A 120 HIS A 122 ASP A 124 HIS A 189 SITE 2 AC1 5 MRI A 303 SITE 1 AC2 4 ASP A 124 CYS A 208 HIS A 250 MRI A 303 SITE 1 AC3 11 PHE A 70 HIS A 120 HIS A 122 GLN A 123 SITE 2 AC3 11 ASP A 124 HIS A 189 GLY A 219 ASN A 220 SITE 3 AC3 11 HIS A 250 ZN A 301 ZN A 302 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