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(-) Description

Title :  CRYSTAL STRUCTURE OF NDM-1 BOUND TO ETHYLENE GLYCOL
 
Authors :  N. C. J. Strynadka, D. T. King
Date :  01 May 12  (Deposition) - 08 Aug 12  (Release) - 15 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.47
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Metallo-Beta-Lactamase, Antibiotic, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. T. King, L. J. Worrall, R. Gruninger, N. C. Strynadka
New Delhi Metallo-Beta-Lactamase: Structural Insights Into Beta-Lactam Recognition And Inhibition
J. Am. Chem. Soc. V. 134 11362 2012
PubMed-ID: 22713171  |  Reference-DOI: 10.1021/JA303579D

(-) Compounds

Molecule 1 - BETA-LACTAMASE NDM-1
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BLANDM-1
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573
    Synonym: NDM-1, 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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:122 , ASP A:124 , HIS A:189 , ASN A:220 , ZN A:302 , ZN A:303BINDING SITE FOR RESIDUE EDO A 301
2AC2SOFTWAREASP A:124 , CYS A:208 , HIS A:250 , EDO A:301 , ZN A:303BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREHIS A:120 , HIS A:122 , HIS A:189 , EDO A:301 , ZN A:302BINDING SITE FOR RESIDUE ZN A 303
4AC4SOFTWAREHIS B:122 , ASP B:124 , HIS B:189 , ASN B:220 , HIS B:250 , ZN B:302 , ZN B:303BINDING SITE FOR RESIDUE EDO B 301
5AC5SOFTWAREASP B:124 , CYS B:208 , HIS B:250 , EDO B:301 , ZN B:303BINDING SITE FOR RESIDUE ZN B 302
6AC6SOFTWAREHIS B:120 , HIS B:122 , HIS B:189 , EDO B:301 , ZN B:302BINDING SITE FOR RESIDUE ZN B 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe B:70 -Gly B:71

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EXY)

(-) 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 d4exya_ A: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeeeee..eeeeeee.........eeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eee.hhhh.................hhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4exy A  42 GDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLRLV 272
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271 


Chain B from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains d4exyb_ B: automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....eee..eeeeeee..eeeeeeeee.....eeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eee......................hhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4exy B  34 TIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLRLV 272
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BLAN1_KLEPN | C7C422: 3pg4 3q6x 3rkj 3rkk 3sbl 3sfp 3spu 3srx 3zr9 4exs 4ey2 4eyb 4eyf 4eyl 4gyq 4gyu 4h0d 4hky 4hl1 4hl2 4ram 4raw 4rbs 4rl0 4rl2 4rm5 4u4l 5a5z 5jqj 5k4k 5k4m 5k4n 5n0h 5n0i

(-) Related Entries Specified in the PDB File

3q6x 3spu 4exs 4ey2 4eyb 4eyf 4eyl