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(-) Description

Title :  VIM-2 METALLO-BETA-LACTAMASE IN COMPLEX WITH ((S)-3-MERCAPTO-2-METHYLPROPANOYL)-D-TRYPTOPHAN (COMPOUND 3)
 
Authors :  G. -B. Li, J. Brem, M. A. Mcdonough, C. J. Schofield
Date :  11 Feb 17  (Deposition) - 17 May 17  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Metallo-Beta-Lactamase, Inhibitor, Complex, Antibiotic Resistance, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. B. Li, J. Brem, R. Lesniak, M. I. Abboud, C. T. Lohans, I. J. Clifton, S. Y. Yang, J. C. Jimenez-Castellanos, M. B. Avison, J. Spencer, M. A. Mcdonough, C. J. Schofield
Crystallographic Analyses Of Isoquinoline Complexes Reveal New Mode Of Metallo-Beta-Lactamase Inhibition.
Chem. Commun. (Camb. ) V. 53 5806 2017
PubMed-ID: 28470248  |  Reference-DOI: 10.1039/C7CC02394D

(-) Compounds

Molecule 1 - BETA-LACTAMASE VIM-2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: OPINF VECTOR BASED
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector Type: PLASMID
    Gene: BLAVIM-2, BLA VIM-2, BLA-VIM-2, BLASVIM-2, BLAVIM2, BLM, VIM- 2, VIM-2, PAERUG_P32_LONDON_17_VIM_2_10_11_06255
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: CLASS B BETA-LACTAMASE,CLASS B CARBAPENEMASE VIM-2,METALLO BETA LACTAMASE VIM-2,METALLO BETA-LACTAMASE,METALLO-BETA-LACTAMASE, METALLO-BETA-LACTAMASE VIM-2,METALLO-BETA-LACTAMASE VIM-2,VIM-2 METALLO-BETA-LACTAMASE,VIM-2 PROTEIN

 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
1FMT6Ligand/IonFORMIC ACID
2R382Ligand/Ion(2~{R})-3-(1~{H}-INDOL-3-YL)-2-[[(2~{S})-2-METHYL-3-SULFANYL-PROPANOYL]AMINO]PROPANOIC ACID
3ZN6Ligand/IonZINC ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2R381Ligand/Ion(2~{R})-3-(1~{H}-INDOL-3-YL)-2-[[(2~{S})-2-METHYL-3-SULFANYL-PROPANOYL]AMINO]PROPANOIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1FMT4Ligand/IonFORMIC ACID
2R381Ligand/Ion(2~{R})-3-(1~{H}-INDOL-3-YL)-2-[[(2~{S})-2-METHYL-3-SULFANYL-PROPANOYL]AMINO]PROPANOIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:118 , CYS A:198 , HIS A:240 , R38 A:504binding site for residue ZN A 501
02AC2SOFTWAREHIS A:114 , HIS A:116 , HIS A:179 , R38 A:504binding site for residue ZN A 502
03AC3SOFTWAREHIS A:251 , FMT A:505 , FMT A:506binding site for residue ZN A 503
04AC4SOFTWARETRP A:87 , HIS A:116 , ASP A:118 , HIS A:179 , ARG A:205 , GLY A:209 , ASN A:210 , HIS A:240 , ZN A:501 , ZN A:502 , HOH A:650 , HOH A:687 , GLY B:64binding site for residue R38 A 504
05AC5SOFTWAREHIS A:251 , ZN A:503 , FMT A:506 , HOH A:619binding site for residue FMT A 505
06AC6SOFTWAREHIS A:251 , ASN A:254 , ZN A:503 , FMT A:505binding site for residue FMT A 506
07AC7SOFTWAREASP B:118 , CYS B:198 , HIS B:240 , R38 B:504binding site for residue ZN B 501
08AC8SOFTWAREHIS B:114 , HIS B:116 , HIS B:179 , R38 B:504binding site for residue ZN B 502
09AC9SOFTWAREHIS B:153 , HIS B:251 , FMT B:505 , FMT B:506binding site for residue ZN B 503
10AD1SOFTWAREGLY A:64 , ALA A:65 , TRP B:87 , HIS B:116 , ASP B:118 , HIS B:179 , ARG B:205 , ASN B:210 , HIS B:240 , ZN B:501 , ZN B:502 , HOH B:614 , HOH B:642 , HOH B:678binding site for residue R38 B 504
11AD2SOFTWAREALA B:132 , HIS B:153 , HIS B:251 , ASN B:254 , ZN B:503 , FMT B:506 , HOH B:646binding site for residue FMT B 505
12AD3SOFTWAREALA B:132 , THR B:152 , HIS B:153 , HIS B:251 , ZN B:503 , FMT B:505 , HOH B:632binding site for residue FMT B 506
13AD4SOFTWARELYS A:101 , GLN A:102 , ILE A:103 , GLY A:104 , PRO B:137 , ARG B:141binding site for residue FMT B 507
14AD5SOFTWAREGLY B:245 , LEU B:246 , ASP B:247binding site for residue FMT B 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5N4S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5N4S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5N4S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5N4S)

(-) Exons   (0, 0)

(no "Exon" information available for 5N4S)

(-) 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:232
                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....eeeeee..eeeeeeeeee..eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeehhhhhhhhhhhh.....ee........eeeee..eeeee..........eeee....eeeeehhh.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5n4s A  32 AYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRA 263
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261  


Chain B from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....eeeeee..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
                 5n4s B  32 AYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNR 262
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5N4S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5N4S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5N4S)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        Q9K2N0_PSEAI | Q9K2N0: 5k48 5n4t 5nhz 5ni0
UniProtKB/TrEMBL
        Q9K2N0_PSEAI | Q9K2N0: 1ko2 1ko3 4bz3 4c1d 4c1e 4nq2 4pvo 4pvt 4ua4 5acu 5acv 5acw 5acx 5fqc 5lca 5lcf 5lch 5le1 5lm6

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