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(-) Description

Title :  STRUCTURAL AND MECHANISTIC INSIGHTS INTO NDM-1 CATALYZED HYDROLYSIS OF CEPHALOSPORINS
 
Authors :  H. Feng, J. Ding, D. Zhu, X. Liu, X. Xu, Y. Zhang, S. Zang, D. -C. Wang, W. Li
Date :  15 Oct 14  (Deposition) - 19 Nov 14  (Release) - 19 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ndm-1 Antibiotic Hydrolysis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Feng, J. Ding, D. Zhu, X. Liu, X. Xu, Y. Zhang, S. Zang, D. C. Wang, W. Li
Structural And Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis Of Cephalosporins.
J. Am. Chem. Soc. V. 136 14694 2014
PubMed-ID: 25268575  |  Reference-DOI: 10.1021/JA508388E

(-) 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/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
13S32Ligand/Ion(1R)-2-({(R)-CARBOXY[(2R,5S)-4-CARBOXY-5-METHYL-5,6-DIHYDRO-2H-1,3-THIAZIN-2-YL]METHYL}AMINO)-2-OXO-1-PHENYLETHANAMINIUM
2ZN4Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:120 , HIS A:122 , HIS A:189 , 3S3 A:303 , HOH A:561BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREASP A:124 , CYS A:208 , HIS A:250 , 3S3 A:303 , HOH A:561BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWARETRP 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:301 , ZN A:302 , HOH A:548 , HOH A:550 , HOH A:551 , HOH A:561 , HOH A:584 , THR B:34 , PRO B:68 , GLY B:69BINDING SITE FOR RESIDUE 3S3 A 303
4AC4SOFTWAREHIS B:120 , HIS B:122 , HIS B:189 , 3S3 B:303 , HOH B:599BINDING SITE FOR RESIDUE ZN B 301
5AC5SOFTWAREASP B:124 , CYS B:208 , HIS B:250 , 3S3 B:303 , HOH B:599BINDING SITE FOR RESIDUE ZN B 302
6AC6SOFTWARETHR 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:301 , ZN B:302 , HOH B:411 , HOH B:474 , HOH B:564 , HOH B:599BINDING SITE FOR RESIDUE 3S3 B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RL2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RL2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RL2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RL2)

(-) Exons   (0, 0)

(no "Exon" information available for 4RL2)

(-) Sequences/Alignments

Asymmetric/Biological 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee..eeeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eee......................hhhhhhhhhhhhh....eeee..eeee.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rl2 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee..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
                 4rl2 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)
  - → 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 4RL2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RL2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RL2)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4rl2
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  BLAN1_KLEPN | C7C422
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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 4eyf 4eyl 4gyq 4gyu 4h0d 4hky 4hl1 4hl2 4ram 4raw 4rbs 4rl0 4rm5 4u4l 5a5z 5jqj 5k4k 5k4m 5k4n 5n0h 5n0i

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4RL2)