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(-) Description

Title :  CRYSTAL STRUCTURE OF OXA-163 COMPLEXED WITH IODIDE IN THE ACTIVE SITE
 
Authors :  V. Stojanoski, L. Hu, T. G. Palzkill, B. Prasad
Date :  21 Jan 15  (Deposition) - 22 Jul 15  (Release) - 22 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.87
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Globular, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Stojanoski, D. C. Chow, B. Fryszczyn, L. Hu, P. Nordmann, L. Poirel, B. Sankaran, B. V. Prasad, T. Palzkill
Structural Basis For Different Substrate Profiles Of Two Closely Related Class D Beta-Lactamases And Their Inhibitio By Halogens.
Biochemistry V. 54 3370 2015
PubMed-ID: 25938261  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00298

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A, B, C, D
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 25-261
    Gene: BLAOXA-163
    Organism Scientific: ENTEROBACTER CLOACAE
    Organism Taxid: 550

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 20)

Asymmetric Unit (1, 20)
No.NameCountTypeFull Name
1IOD20Ligand/IonIODIDE ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1IOD12Ligand/IonIODIDE ION
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1IOD8Ligand/IonIODIDE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:157BINDING SITE FOR RESIDUE IOD A 301
02AC2SOFTWAREARG A:206 , ARG D:206BINDING SITE FOR RESIDUE IOD A 302
03AC3SOFTWAREARG A:186BINDING SITE FOR RESIDUE IOD A 303
04AC4SOFTWAREASN A:48 , LYS A:51 , LYS C:51BINDING SITE FOR RESIDUE IOD A 304
05AC5SOFTWAREASN A:32BINDING SITE FOR RESIDUE IOD A 305
06AC6SOFTWARELEU A:67BINDING SITE FOR RESIDUE IOD A 306
07AC7SOFTWARELYS A:180BINDING SITE FOR RESIDUE IOD A 307
08AC8SOFTWAREARG B:206 , ARG C:206BINDING SITE FOR RESIDUE IOD B 301
09AC9SOFTWARETRP B:157BINDING SITE FOR RESIDUE IOD B 302
10BC1SOFTWARELEU B:67BINDING SITE FOR RESIDUE IOD B 303
11BC2SOFTWARELEU C:67BINDING SITE FOR RESIDUE IOD C 304
12BC3SOFTWARETRP D:157BINDING SITE FOR RESIDUE IOD D 301
13BC4SOFTWAREHIS D:178 , LYS D:180BINDING SITE FOR RESIDUE IOD D 303
14BC5SOFTWARELEU D:67BINDING SITE FOR RESIDUE IOD D 304
15BC6SOFTWAREGLN D:41 , GLY D:42BINDING SITE FOR RESIDUE IOD D 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4S2M)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly B:160 -Gly B:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4S2M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S2M)

(-) Exons   (0, 0)

(no "Exon" information available for 4S2M)

(-) 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 .ee...hhhhhhh....eeeeeee....eeee...hhhh.ee.hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeee.......eeeeeeeee....eeeeeeeee...hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s2m A  25 WQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYDTKIGWWVGWVELDDNVWFFAMNMDMPGLRQAITKEVLKQEKIIP 265
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       218       228       238   ||  253       263  
                                                                                                                                                                                                                      213|                     242|                 
                                                                                                                                                                                                                       218                      248                 


Chain B from PDB  Type:PROTEIN  Length:234
                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee...hhhhhhh....eeeeeee....eeee...hhhh.ee.hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh...eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeee.......eeeeeeeee....eeeeeeeee.....hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4s2m B  25 WQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYDTKIGWWVGWVELDDNVWFFAMNMDMPGLGLRQAITKEVLKQEKIIP 265
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       218       228       238   ||  251       261    
                                                                                                                                                                                                                      213|                     242|                   
                                                                                                                                                                                                                       218                      246                   


Chain C from PDB  Type:PROTEIN  Length:234
                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee...hhhhhhh....eeeeeee....eeee...hhhh.ee.hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeee.......eeeeeeeee....eeeeeeeee.....hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4s2m C  25 WQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYDTKIGWWVGWVELDDNVWFFAMNMDMPGLGLRQAITKEVLKQEKIIP 265
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       218       228       238   ||  251       261    
                                                                                                                                                                                                                      213|                     242|                   
                                                                                                                                                                                                                       218                      246                   


Chain D from PDB  Type:PROTEIN  Length:234
                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee...hhhhhhh....eeeeeee....eeee...hhhh.ee.hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeee.......eeeeeeeee....eeeeeeeee.....hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4s2m D  25 WQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYDTKIGWWVGWVELDDNVWFFAMNMDMPTSGLRQAITKEVLKQEKIIP 265
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       218       228       238     ||251       261    
                                                                                                                                                                                                                      213|                       244|                 
                                                                                                                                                                                                                       218                        248
   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 4S2M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S2M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S2M)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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        F6KZJ2_ENTCL | F6KZJ2: 4s2l 5har

(-) Related Entries Specified in the PDB File

4s2l THE SAME PROTEIN AT 1.72A WITHOUT IODINE IN THE ACTIVE SITE