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(-) Description

Title :  VIM-2_10C. 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 :  22 Mar 17  (Deposition) - 26 Apr 17  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym. Unit :  A,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  E  (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 - BETA-LACTAMASE CLASS B VIM-2
    Chains: A, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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: BLAVIM-2,CLASS B CARBAPENEMASE VIM-2,METALLO BETA-LACTAMASE, METALLO-BETA LACTAMASE PROTEIN,METALLO-BETA-LACTAMASE VIM-2,VIM-2, VIM-2 BETA-LACTAMASE,VIM-2 CLASS B METALLO B-LACTAMASE,VIM-2 TYPE METALLO-BETA-LACTAMASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AE
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
18XW2Ligand/Ion[(2~{R})-1-ETHANOYLSULFANYL-6-PHENYL-HEXAN-2-YL]PHOSPHONIC ACID
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
18XW1Ligand/Ion[(2~{R})-1-ETHANOYLSULFANYL-6-PHENYL-HEXAN-2-YL]PHOSPHONIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
18XW1Ligand/Ion[(2~{R})-1-ETHANOYLSULFANYL-6-PHENYL-HEXAN-2-YL]PHOSPHONIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:116 , HIS A:118 , HIS A:196 , 8XW A:403 , HOH A:527binding site for residue ZN A 401
2AC2SOFTWAREASP A:120 , ARG A:121 , CYS A:221 , HIS A:263 , 8XW A:403 , HOH A:527binding site for residue ZN A 402
3AC3SOFTWAREPHE A:61 , TYR A:67 , TRP A:87 , ASP A:120 , HIS A:196 , CYS A:221 , ARG A:228 , HIS A:263 , ZN A:401 , ZN A:402 , HOH A:527 , HOH A:644 , HOH E:651binding site for residue 8XW A 403
4AC4SOFTWAREHIS E:116 , HIS E:118 , HIS E:196 , 8XW E:403 , HOH E:507binding site for residue ZN E 401
5AC5SOFTWAREASP E:120 , ARG E:121 , CYS E:221 , HIS E:263 , 8XW E:403 , HOH E:507binding site for residue ZN E 402
6AC6SOFTWAREPHE E:61 , TYR E:67 , TRP E:87 , HIS E:118 , ASP E:119 , ASP E:120 , HIS E:196 , CYS E:221 , ARG E:228 , ASN E:233 , HIS E:263 , ZN E:401 , ZN E:402 , HOH E:507 , HOH E:527binding site for residue 8XW E 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5NI0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5NI0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5NI0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5NI0)

(-) Exons   (0, 0)

(no "Exon" information available for 5NI0)

(-) 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:230
                                                                                                                                                                                                                                                                      
               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
                 5ni0 A  30 EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTN 295
                                    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 E from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               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.........hhhhh...hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ni0 E  30 EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHT 294
                                    39     || 50        60   ||   71        81        91       102    || 113       123       134       144     ||168       178       188       198      |211|      224       234       244       254       264||     285         
                                          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 5NI0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5NI0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5NI0)

(-) Gene Ontology  (2, 2)

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 Related Entries

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        Q9K2N0_PSEAI | Q9K2N0: 5k48 5n4s 5n4t 5nhz
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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