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(-) Description

Title :  CRYSTAL STRUCTURE OF VIM-2 METALLO-BETA-LACTAMASE IN COMPLEX WITH ML302F
 
Authors :  W. S. Aik, J. Brem, M. A. Mcdonough, C. J. Schofield
Date :  18 Mar 14  (Deposition) - 19 Nov 14  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha-Beta/Beta-Alpha, Beta-Lactamase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Brem, S. S. Van Berkel, W. Aik, A. M. Rydzik, M. B. Avison, I. Pettinati, K. D. Umland, A. Kawamura, J. Spencer, T. D. Claridge, M. A. Mcdonough, C. J. Schofield
Rhodanine Hydrolysis Leads To Potent Thioenolate Mediated Metallo-Beta-Lactamase Inhibition.
Nat. Chem. V. 6 1084 2014
PubMed-ID: 25411887  |  Reference-DOI: 10.1038/NCHEM.2110

(-) Compounds

Molecule 1 - BETA-LACTAMASE CLASS B VIM-2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POPIN-F VIM-2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 27-266
    Gene: BLA-VIM-2, BLASVIM-2, BLAVIM-2, BLAVIM2, VIM-2
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: CLASS B BETA-LACTAMASE, METALLO BETA-LACTAMASE, METALLO- BETA-LACTAMASE, METALLO-BETA-LACTAMASE VIM-2, METTALO-BETA-LACTAMASE VIM-2, VIM-2, VIM-2 CLASS B METALLO B-LACTAMASE, VIM-2 PROTEIN, VIM-2 TYPE METALLO-BETA-LACTAMASE

 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  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1FMT4Ligand/IonFORMIC ACID
2GOL1Ligand/IonGLYCEROL
3S3C2Ligand/Ion(2Z)-2-SULFANYL-3-(2,3,6-TRICHLOROPHENYL)PROP-2-ENOICACID
4ZN6Ligand/IonZINC ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2GOL-1Ligand/IonGLYCEROL
3S3C1Ligand/Ion(2Z)-2-SULFANYL-3-(2,3,6-TRICHLOROPHENYL)PROP-2-ENOICACID
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2GOL1Ligand/IonGLYCEROL
3S3C1Ligand/Ion(2Z)-2-SULFANYL-3-(2,3,6-TRICHLOROPHENYL)PROP-2-ENOICACID
4ZN-1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:116 , HIS A:118 , HIS A:196 , S3C A:403BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWAREASP A:120 , CYS A:221 , HIS A:263 , S3C A:403BINDING SITE FOR RESIDUE ZN A 402
03AC3SOFTWARETRP A:87 , HIS A:118 , ASP A:120 , HIS A:196 , CYS A:221 , ARG A:228 , ASN A:233 , HIS A:263 , ZN A:401 , ZN A:402 , HOH A:501 , HOH A:560BINDING SITE FOR RESIDUE S3C A 403
04AC4SOFTWAREHIS A:170 , HIS A:285 , FMT A:405 , FMT A:406BINDING SITE FOR RESIDUE ZN A 404
05AC5SOFTWAREALA A:135 , THR A:136 , THR A:169 , HIS A:170 , HIS A:285 , ASN A:288 , ZN A:404 , FMT A:406 , HOH A:514BINDING SITE FOR RESIDUE FMT A 405
06AC6SOFTWAREALA A:135 , HIS A:170 , HIS A:285 , ASN A:288 , ZN A:404 , FMT A:405BINDING SITE FOR RESIDUE FMT A 406
07AC7SOFTWAREHIS B:116 , HIS B:118 , HIS B:196 , S3C B:406BINDING SITE FOR RESIDUE ZN B 401
08AC8SOFTWAREASP B:120 , CYS B:221 , HIS B:263 , S3C B:406BINDING SITE FOR RESIDUE ZN B 402
09AC9SOFTWAREHIS B:170 , FMT B:404 , FMT B:405BINDING SITE FOR RESIDUE ZN B 403
10BC1SOFTWAREALA B:135 , HIS B:170 , ZN B:403 , FMT B:405 , HOH B:543BINDING SITE FOR RESIDUE FMT B 404
11BC2SOFTWAREALA B:135 , THR B:136 , THR B:169 , HIS B:170 , ZN B:403 , FMT B:404 , HOH B:509BINDING SITE FOR RESIDUE FMT B 405
12BC3SOFTWARETRP B:87 , HIS B:118 , ASP B:120 , HIS B:196 , CYS B:221 , ASN B:233 , HIS B:263 , ZN B:401 , ZN B:402 , GOL B:407 , HOH B:505 , HOH B:546BINDING SITE FOR RESIDUE S3C B 406
13BC4SOFTWARETYR B:67 , ARG B:228 , HIS B:263 , S3C B:406BINDING SITE FOR RESIDUE GOL B 407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PVT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PVT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PVT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PVT)

(-) Exons   (0, 0)

(no "Exon" information available for 4PVT)

(-) 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: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
                 4pvt A  30 EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNR 296
                                    39     || 50        60   ||   71        81        91       102    || 113       123       134       144     ||168       178       188       198      |211|      224       234       244       254       264||     285       295 
                                          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: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
                 4pvt B  30 EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNR 296
                                    39     || 50        60   ||   71        81        91       102    || 113       123       134       144     ||168       178       188       198      |211|      224       234       244       254       264||     285       295 
                                          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 4PVT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PVT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PVT)

(-) Gene Ontology  (2, 2)

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9K2N0_PSEAI | Q9K2N0: 5k48 5n4s 5n4t 5nhz 5ni0
UniProtKB/TrEMBL
        Q9K2N0_PSEAI | Q9K2N0: 1ko2 1ko3 4bz3 4c1d 4c1e 4nq2 4pvo 4ua4 5acu 5acv 5acw 5acx 5fqc 5lca 5lcf 5lch 5le1 5lm6

(-) Related Entries Specified in the PDB File

1ko2 1ko3 4pvo