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(-) Description

Title :  THE STRUCTURE OF THE METALLO-BETA-LACTAMASE VIM-2 IN COMPLEX WITH A TRIAZOLYLTHIOACETAMIDE INHIBITOR
 
Authors :  T. Christopeit, K. -W. Yang, S. -K. Yang, H. -K. S. Leiros
Date :  25 Aug 16  (Deposition) - 09 Nov 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Antibiotic Resistance, Carbapenemases, Verona Integron-Encoded Metallo-Beta-Lactamase 2, Vim-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Christopeit, K. -W. Yang, S. -K. Yang, H. -K. S. Leiros
The Structure Of The Metallo-Beta-Lactamase Vim-2 In Comple With A Triazolylthioacetamide Inhibitor.
Acta Crystallogr. , Sect. F V. 72 813 2016
PubMed: search  |  Reference-DOI: 10.1107/S2053230X16016113

(-) Compounds

Molecule 1 - METALLO-BETA-LACTAMASE VIM-2-LIKE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PDEST14
    Gene: BLAVIM
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
17522Ligand/Ion2-[5-[2-(1,3-BENZOTHIAZOL-2-YLAMINO)-2-OXIDANYLIDENE-ETHYL]SULFANYL-4~{H}-1,2,4-TRIAZOL-3-YL]BENZOIC ACID
2CL6Ligand/IonCHLORIDE ION
3ZN6Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
17521Ligand/Ion2-[5-[2-(1,3-BENZOTHIAZOL-2-YLAMINO)-2-OXIDANYLIDENE-ETHYL]SULFANYL-4~{H}-1,2,4-TRIAZOL-3-YL]BENZOIC ACID
2CL-1Ligand/IonCHLORIDE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
17521Ligand/Ion2-[5-[2-(1,3-BENZOTHIAZOL-2-YLAMINO)-2-OXIDANYLIDENE-ETHYL]SULFANYL-4~{H}-1,2,4-TRIAZOL-3-YL]BENZOIC ACID
2CL-1Ligand/IonCHLORIDE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:170 , HIS A:285 , ASN A:288 , CL A:402 , ZN A:407binding site for residue CL A 401
02AC2SOFTWAREHIS A:170 , HIS A:285 , CL A:401 , ZN A:407 , HOH A:665binding site for residue CL A 402
03AC3SOFTWAREHIS A:118 , ASP A:119 , ASN A:165 , HOH A:786binding site for residue CL A 403
04AC4SOFTWAREGLN A:59 , TYR A:67 , TRP A:87 , GLY A:88 , HIS A:118 , ASP A:119 , ASP A:120 , HIS A:196 , CYS A:221 , ARG A:228 , GLY A:232 , ASN A:233 , HIS A:263 , ZN A:405 , ZN A:406 , HOH A:562 , HOH A:584 , HOH A:648 , HOH A:661 , HOH A:685 , HOH A:699binding site for residue 752 A 404
05AC5SOFTWAREHIS A:116 , HIS A:118 , ASP A:120 , HIS A:196 , 752 A:404binding site for residue ZN A 405
06AC6SOFTWAREASP A:120 , CYS A:221 , HIS A:263 , 752 A:404binding site for residue ZN A 406
07AC7SOFTWAREHIS A:170 , HIS A:285 , CL A:401 , CL A:402binding site for residue ZN A 407
08AC8SOFTWAREALA B:135 , HIS B:170 , HIS B:285 , ASN B:288 , CL B:402 , ZN B:407 , HOH B:750binding site for residue CL B 401
09AC9SOFTWAREHIS B:170 , HIS B:285 , ASN B:288 , CL B:401 , ZN B:407 , HOH B:527 , HOH B:644binding site for residue CL B 402
10AD1SOFTWAREHIS B:118 , ASP B:119 , ASN B:165binding site for residue CL B 403
11AD2SOFTWAREPHE B:61 , TYR B:67 , TRP B:87 , GLY B:88 , HIS B:118 , ASP B:119 , ASP B:120 , HIS B:196 , CYS B:221 , GLY B:232 , ASN B:233 , HIS B:263 , ZN B:405 , ZN B:406 , HOH B:580 , HOH B:596 , HOH B:656 , HOH B:658 , HOH B:686 , HOH B:760binding site for residue 752 B 404
12AD3SOFTWAREHIS B:116 , HIS B:118 , ASP B:120 , HIS B:196 , 752 B:404binding site for residue ZN B 405
13AD4SOFTWAREASP B:120 , CYS B:221 , HIS B:263 , 752 B:404binding site for residue ZN B 406
14AD5SOFTWAREHIS B:170 , HIS B:285 , CL B:401 , CL B:402 , HOH B:527binding site for residue ZN B 407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LSC)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser B:297 -Val B:298

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LSC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LSC)

(-) Exons   (0, 0)

(no "Exon" information available for 5LSC)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh....eeeeeee..eeeeeeeeee..eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeehhhhhhhhhhhh.....ee.........eeee..eeee...........eeee....eeeeehhh.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lsc A  28 SGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSV 298
                                    37       |48        58     || 69        79        89        99||    |111       121       131|      142       166       176       186       196       209 ||    222       232       242       252       262  ||   283       293     
                                            45|               64|                               100|  107|                   131|              150|                                     205| ||                                               265|                     
                                             47                66                                102   109                    133               165                                      209 ||                                                277                     
                                                                                                                                                                                           211|                                                                        
                                                                                                                                                                                            215                                                                        


Chain B from PDB  Type:PROTEIN  Length:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh....eeeeeee..eeeeeeeeee..eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeehhhhhhhhhhhh.....ee........eeeee..eeeee..........eeee....eeeeehhh.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lsc B  28 SGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSV 298
                                    37       |48        58     || 69        79        89        99||    |111       121       131|      142       166       176       186       196       209 ||    222       232       242       252       262  ||   283       293     
                                            45|               64|                               100|  107|                   131|              150|                                     205| ||                                               265|                     
                                             47                66                                102   109                    133               165                                      209 ||                                                277                     
                                                                                                                                                                                           211|                                                                        
                                                                                                                                                                                            215
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5LSC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LSC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LSC)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5LSC)

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