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(-) Description

Title :  CRYSTAL STRUCTURE OF NEW DELHI METALLO-BETA-LACTAMASE (NDM-1)
 
Authors :  Y. Guo, J. Wang, G. J. Niu, W. Q. Shui, Y. N. Sun, Z. Y. Lou, Z. H. Rao
Date :  13 May 11  (Deposition) - 01 Jun 11  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  New Delhi Metallo-Beta-Lactamase 1, Ndm-1, Drug Resistant, Drug Discovery, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Guo, J. Wang, G. Niu, W. Shui, Y. Sun, H. Zhou, Y. Zhang, C. Yang, Z. Lou Z. Rao
A Structural View Of The Antibiotic Degradation Enzyme Ndm- From A Superbug.
Protein Cell 2011
PubMed-ID: 21637961  |  Reference-DOI: 10.1007/S13238-011-1055-9

(-) Compounds

Molecule 1 - METALLO-BETA-LACTAMASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 47-270
    Gene: BLANDM-1
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: NEW DELHI METALLO-BETA-LACTAMASE, NDM-1

 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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:124 , CYS A:208 , HIS A:250 , HOH A:368 , ZN A:1002BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWAREHIS A:120 , HIS A:122 , ASP A:124 , HIS A:189 , CYS A:208 , ZN A:1001BINDING SITE FOR RESIDUE ZN A 1002
3AC3SOFTWAREASP B:124 , CYS B:208 , HIS B:250 , HOH B:341BINDING SITE FOR RESIDUE ZN B 1001
4AC4SOFTWAREHIS B:120 , HIS B:122 , ASP B:124 , HIS B:189 , CYS B:208BINDING SITE FOR RESIDUE ZN B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S0Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3S0Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S0Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S0Z)

(-) Exons   (0, 0)

(no "Exon" information available for 3S0Z)

(-) 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:220
 aligned with E5KIY2_ECOLX | E5KIY2 from UniProtKB/TrEMBL  Length:270

    Alignment length:224
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266    
         E5KIY2_ECOLX    47 GDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
               SCOP domains d3s0za_ A: automated matches                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee......eeeee..............eeeeee..eeeee........hhhhhhhhhh.....eeeeee.........hhhhhhhh..eeeee................eee.....----.........eeee...........eeee....eeeee.................hhhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s0z A  47 GDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAAN----PATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    56        66        76        86        96       106       116       126       136       146       156       166    |  176       186       196       206       216       226       236       246       256       266    
                                                                                                                                                 166  171                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:220
 aligned with E5KIY2_ECOLX | E5KIY2 from UniProtKB/TrEMBL  Length:270

    Alignment length:224
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266    
         E5KIY2_ECOLX    47 GDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
               SCOP domains d3s0zb_ B: automated matches                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------Lactamase_B-3s0zB01 B:70-250                                                                                                                                                         -------------------- Pfam domains (1)
           Pfam domains (2) -----------------------Lactamase_B-3s0zB02 B:70-250                                                                                                                                                         -------------------- Pfam domains (2)
         Sec.struct. author ..eeeeeee..eeeeeeee.......eeee.eeeee..eeeee....hhhhhhhhhhhhhh.....eeeee..........hhhhhhhhh.eee.hhhhh..hhhhh.............----.........eeee...........eeee....eeeee.................hhhhhhhhhh..........eeee........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s0z B  47 GDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAAN----PATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    56        66        76        86        96       106       116       126       136       146       156       166    |  176       186       196       206       216       226       236       246       256       266    
                                                                                                                                                 166  171
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S0Z)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Metallo-HOrase (67)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (E5KIY2_ECOLX | E5KIY2)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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