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(-) Description

Title :  CRYSTAL STRUCTURE OF NDM-1 BOUND TO HYDROLYZED BENZYLPENICILLIN
 
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 :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Metallo Beta Lactamase, Antibiotic, Hydrolase-Antibiotic Complex (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
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1PNK2Ligand/Ion(2R,4S)-2-{(R)-CARBOXY[(PHENYLACETYL)AMINO]METHYL}-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
2ZN6Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PNK1Ligand/Ion(2R,4S)-2-{(R)-CARBOXY[(PHENYLACETYL)AMINO]METHYL}-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PNK1Ligand/Ion(2R,4S)-2-{(R)-CARBOXY[(PHENYLACETYL)AMINO]METHYL}-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1PNK1Ligand/Ion(2R,4S)-2-{(R)-CARBOXY[(PHENYLACETYL)AMINO]METHYL}-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:65 , MET A:67 , TRP A:93 , HIS A:122 , GLN A:123 , ASP A:124 , HIS A:189 , CYS A:208 , LYS A:211 , GLY A:219 , ASN A:220 , HIS A:250 , ZN A:302 , ZN A:303 , HOH A:401 , HOH A:489 , HOH A:491 , THR B:34 , GLY B:69BINDING SITE FOR RESIDUE PNK A 301
2AC2SOFTWAREHIS A:120 , HIS A:122 , HIS A:189 , PNK A:301 , HOH A:401BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREASP A:124 , CYS A:208 , HIS A:250 , PNK A:301BINDING SITE FOR RESIDUE ZN A 303
4AC4SOFTWAREGLU A:152 , ASP A:223 , HOH A:475 , GLU B:227BINDING SITE FOR RESIDUE ZN A 304
5AC5SOFTWARETHR A:34 , GLY A:69 , LEU B:65 , MET B:67 , TRP B:93 , HIS B:122 , GLN B:123 , ASP B:124 , HIS B:189 , CYS B:208 , LYS B:211 , GLY B:219 , ASN B:220 , HIS B:250 , ZN B:302 , ZN B:303 , HOH B:401 , HOH B:427 , HOH B:441BINDING SITE FOR RESIDUE PNK B 301
6AC6SOFTWAREASP B:124 , CYS B:208 , HIS B:250 , PNK B:301 , HOH B:401BINDING SITE FOR RESIDUE ZN B 302
7AC7SOFTWAREHIS B:120 , HIS B:122 , HIS B:189 , PNK B:301 , HOH B:401BINDING SITE FOR RESIDUE ZN B 303
8AC8SOFTWAREGLU A:227 , GLU B:152 , ASP B:223 , HOH B:488BINDING SITE FOR RESIDUE ZN B 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EYF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EYF)

(-) 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:241
                                                                                                                                                                                                                                                                                 
               SCOP domains d4eyfa_ A: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee..eeeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eeeee....................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eyf A  30 EIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269 


Chain B from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains d4eyfb_ B: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee..eeeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eee......................hhhhhhhhhhhhh....eee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eyf B  30 EIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269
   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 4EYF)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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  3.5.2.6
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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 4exy 4ey2 4eyb 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 4exy 4ey2 4eyb 4eyl