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(-) Description

Title :  VIM-2_2B. METALLO-BETA-LACTAMASE INHIBITORS BY BIOISOSTERIC REPLACEMENT: PREPARATION, ACTIVITY AND BINDING
 
Authors :  S. Skagseth, S. Akhter, M. H. Paulsen, O. Samuelsen, Z. Muhammad, H. -K. A. Bayer
Date :  08 Dec 16  (Deposition) - 29 Mar 17  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Inhibition Properties, Bioisosters, Thiols, Metallo-Beta-Lactamase Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Skagseth, S. Akhter, M. H. Paulsen, Z. Muhammad, S. Lauksund, H. S. Leiros, A. Bayer
Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity And Binding.
Eur J Med Chem V. 135 159 2017
PubMed-ID: 28445786  |  Reference-DOI: 10.1016/J.EJMECH.2017.04.035

(-) Compounds

Molecule 1 - METALLO-BETA-LACTAMASE VIM-17
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR PLYSS
    Gene: BLAVIM-17
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: VERONA INTEGRON-ENCODED 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  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
18SH2Ligand/Ion(2~{R})-2-DIETHOXYPHOSPHORYL-5-PHENYL-PENTANE-1-THIOL
2MG1Ligand/IonMAGNESIUM ION
3ZN6Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
18SH1Ligand/Ion(2~{R})-2-DIETHOXYPHOSPHORYL-5-PHENYL-PENTANE-1-THIOL
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
18SH1Ligand/Ion(2~{R})-2-DIETHOXYPHOSPHORYL-5-PHENYL-PENTANE-1-THIOL
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:116 , HIS A:118 , HIS A:196 , ZN A:402 , 8SH A:404binding site for residue ZN A 401
2AC2SOFTWAREASP A:120 , CYS A:221 , HIS A:263 , ZN A:401 , 8SH A:404binding site for residue ZN A 402
3AC3SOFTWAREHIS A:170 , HIS A:285 , HOH A:517 , HOH A:703binding site for residue ZN A 403
4AC4SOFTWAREPHE A:61 , TYR A:67 , TRP A:87 , HIS A:118 , ASP A:120 , HIS A:196 , ARG A:228 , ASN A:233 , HIS A:263 , ZN A:401 , ZN A:402 , HOH A:640binding site for residue 8SH A 404
5AC5SOFTWAREHIS B:116 , HIS B:118 , HIS B:196 , 8SH B:405binding site for residue ZN B 401
6AC6SOFTWAREASP B:120 , ARG B:121 , CYS B:221 , HIS B:263 , 8SH B:405binding site for residue ZN B 402
7AC7SOFTWARETHR B:115 , HIS B:116 , GLY B:220 , CYS B:221 , HOH B:577binding site for residue MG B 403
8AC8SOFTWAREHIS B:170 , HIS B:285 , HOH B:701 , HOH B:708binding site for residue ZN B 404
9AC9SOFTWAREASP A:62 , PHE B:61 , TYR B:67 , TRP B:87 , HIS B:118 , ASP B:119 , ASP B:120 , HIS B:196 , ARG B:228 , ASN B:233 , HIS B:263 , ZN B:401 , ZN B:402binding site for residue 8SH B 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5MM9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5MM9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5MM9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MM9)

(-) Exons   (0, 0)

(no "Exon" information available for 5MM9)

(-) 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
                 5mm9 A  30 EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRS 297
                                    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........eeeee..eeeee..........eeee....eeeeehhh.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mm9 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
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  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 5MM9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MM9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MM9)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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