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(-) Description

Title :  CRYSTAL STRUCTURE OF NEW DELHI METALLO-BETA-LACTAMASE-1 MUTANT M67V COMPLEXED WITH HYDROLYZED PENICILLIN G
 
Authors :  Y. Kim, C. Tesar, R. Jedrzejczak, G. Babnigg, J. Sacchettini, A. Joachi Midwest Center For Structural Genomics (Mcsg), Structures Of Proteins Conferring Susceptibility To Known Mtb Inhibitors
Date :  10 Sep 14  (Deposition) - 24 Sep 14  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Structures Of Mtb Proteins Conferring Susceptibility To Known Mtb Inhibitors, Mtbi, Alpha-Beta-Beta-Alpha Sandwich, Hydrolase, Hydrolase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, C. Tesar, R. Jedrzejczak, G. Babnigg, J. Sacchettini, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg), Structures Of Mtb Proteins Conferring Susceptibility To Known Mtb Inhibitors (Mtbi)
Crystal Structure Of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed With Hydrolyzed Penicillin G
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BETA-LACTAMASE NDM-1
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG50
    Expression System Strain: BL21(DE3) GOLD
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BLANDM-1
    Mutation: YES
    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): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2PNM2Ligand/IonOPEN FORM - PENICILLIN G
3ZN7Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2PNM1Ligand/IonOPEN FORM - PENICILLIN G
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2PNM1Ligand/IonOPEN FORM - PENICILLIN G
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2PNM2Ligand/IonOPEN FORM - PENICILLIN G
3ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:124 , CYS A:208 , HIS A:250 , PNM A:304 , HOH A:559BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREHIS A:120 , HIS A:122 , HIS A:189 , PNM A:304 , HOH A:559BINDING SITE FOR RESIDUE ZN A 302
03AC3SOFTWAREGLU A:152 , ASP A:223 , CL A:305 , GLU B:227BINDING SITE FOR RESIDUE ZN A 303
04AC4SOFTWARELEU A:65 , 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:301 , ZN A:302 , HOH A:559 , THR B:34 , GLY B:69 , PHE B:70BINDING SITE FOR RESIDUE PNM A 304
05AC5SOFTWAREGLU A:152 , ZN A:303 , GLU B:227BINDING SITE FOR RESIDUE CL A 305
06AC6SOFTWAREASP B:124 , CYS B:208 , HIS B:250 , PNM B:304 , HOH B:521BINDING SITE FOR RESIDUE ZN B 301
07AC7SOFTWAREHIS B:120 , HIS B:122 , HIS B:189 , PNM B:304 , HOH B:521BINDING SITE FOR RESIDUE ZN B 302
08AC8SOFTWAREGLU A:227 , GLU B:152 , ASP B:223 , CL B:306BINDING SITE FOR RESIDUE ZN B 303
09AC9SOFTWARETHR A:34 , PRO A:68 , GLY A:69 , PHE A:70 , LEU B:65 , 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:401 , HOH B:501 , HOH B:521BINDING SITE FOR RESIDUE PNM B 304
10BC1SOFTWAREHIS B:159 , HOH B:411 , HOH B:450 , HOH B:569BINDING SITE FOR RESIDUE ZN B 305
11BC2SOFTWAREGLU A:227 , GLU B:152 , ASP B:223 , ZN B:303BINDING SITE FOR RESIDUE CL B 306

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RAM)

(-) 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:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4ram A  31 IRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDVPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKL 269
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         


Chain B from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4ram B  31 IRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDVPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKL 269
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
   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  (0, 0)

(no "SCOP Domain" information available for 4RAM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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  4ram
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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 4raw 4rbs 4rl0 4rl2 4rm5 4u4l 5a5z 5jqj 5k4k 5k4m 5k4n 5n0h 5n0i

(-) Related Entries Specified in the PDB File

3rkj NDM1, DELTA-38 CONSTRUCT
3rkk NDM1, DELTA-36NY CONSTRUCT
3sbl NDM1, DELTA-36NY CONSTRUCT, DIFFERENT CRYSTALS FORM
3sfp NDM1, DELTA-36NY CONSTRUCT, ONE-ZN-BOUND
3srx NDM1, DELTA-36NY CONSTRUCT, TWO-CD-BOUND
4gyq NDM1, DELTA-30 CONSTRUCT, D223A MUTANT
4gyu NDM1, DELTA-30 CONSTRUCT, A121F MUTANT
4h0d NDM1, DELTA-30 CONSTRUCT, TWO MN-BOUND AND HYDROLIZED AMPICILLIN
4hky NDM1, DELTA-30 CONSTRUCT, TWO CD-BOUND AND PARTIAL FAROPENEM
4hl1 NDM1, DELTA-30 CONSTRUCT, TWO CD-BOUND AND PARTIAL AMPICILLIN
4hl2 NDM1, DELTA-30 CONSTRUCT, 1.05 A, COMPLEXED WITH HYDROLIZED AMPICILLIN RELATED ID: MCSG-APC105101 RELATED DB: TARGETTRACK
4raw