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(-) Description

Title :  CRYSTAL STRUCTURE OF NEW DELHI METALLO-BETA-LACTAMASE-1, COMPLEXED WITH CD AND AMPICILLIN
 
Authors :  Y. Kim, C. Tesar, R. Jedrzejczak, J. Babnigg, J. Mire, J. Sacchettini, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg), Structures Of Mtb Proteins Conferring Susceptibility To Kno Inhibitors (Mtbi)
Date :  15 Oct 12  (Deposition) - 12 Dec 12  (Release) - 12 Dec 12  (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, J. Babnigg, J. Mire, J. Sacchettini, A. Joachimiak
Crystal Structure Of New Delhi Metallo-Beta-Lactamase-1, Complexed With Cd And Ampicillin
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: PMCSG7
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    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): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1CD6Ligand/IonCADMIUM ION
2CL2Ligand/IonCHLORIDE ION
3ZZ72Ligand/Ion(2R,4S)-2-[(R)-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}(CARBOXY)METHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3ZZ71Ligand/Ion(2R,4S)-2-[(R)-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}(CARBOXY)METHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3ZZ71Ligand/Ion(2R,4S)-2-[(R)-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}(CARBOXY)METHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3ZZ72Ligand/Ion(2R,4S)-2-[(R)-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}(CARBOXY)METHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:122 , GLN A:123 , ASP A:124 , CYS A:208 , LYS A:211 , GLY A:219 , ASN A:220 , HIS A:250 , CD A:303 , CL A:305 , HOH A:450 , HOH A:484 , THR B:34 , GLY B:69 , PHE B:70BINDING SITE FOR RESIDUE ZZ7 A 301
02AC2SOFTWAREHIS A:120 , HIS A:122 , HIS A:189 , CYS A:208 , CL A:305 , HOH A:484BINDING SITE FOR RESIDUE CD A 302
03AC3SOFTWAREASP A:124 , CYS A:208 , HIS A:250 , ZZ7 A:301 , HOH A:484BINDING SITE FOR RESIDUE CD A 303
04AC4SOFTWAREGLU A:152 , ASP A:223 , HOH A:413 , GLU B:227 , HOH B:463BINDING SITE FOR RESIDUE CD A 304
05AC5SOFTWAREHIS A:122 , HIS A:189 , ZZ7 A:301 , CD A:302BINDING SITE FOR RESIDUE CL A 305
06AC6SOFTWARETHR A:34 , GLY A:69 , PHE A:70 , TRP B:93 , HIS B:122 , GLN B:123 , ASP B:124 , CYS B:208 , LYS B:211 , GLY B:219 , ASN B:220 , HIS B:250 , CD B:303 , CL B:305 , HOH B:624BINDING SITE FOR RESIDUE ZZ7 B 301
07AC7SOFTWAREHIS B:120 , HIS B:122 , HIS B:189 , CYS B:208 , CD B:303 , CL B:305 , HOH B:624BINDING SITE FOR RESIDUE CD B 302
08AC8SOFTWAREASP B:124 , CYS B:208 , HIS B:250 , ZZ7 B:301 , CD B:302 , HOH B:624BINDING SITE FOR RESIDUE CD B 303
09AC9SOFTWAREGLU A:227 , GLU B:152 , ASP B:223 , HOH B:462BINDING SITE FOR RESIDUE CD B 304
10BC1SOFTWAREHIS B:122 , HIS B:189 , ZZ7 B:301 , CD B:302BINDING SITE FOR RESIDUE CL B 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HL1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HL1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HL1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HL1)

(-) Exons   (0, 0)

(no "Exon" information available for 4HL1)

(-) 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:238
                                                                                                                                                                                                                                                                              
               SCOP domains d4hl1a_ A: automated matches                                                                                                                                                                                                                   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
                 4hl1 A  32 RPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKL 269
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261        


Chain B from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains d4hl1b_ 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
                 4hl1 B  31 IRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
   Legend:   → Mismatch (orange background)
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    → 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 4HL1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HL1)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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  4hl1
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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 4hl2 4ram 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 RELATED ID: MCSG-APC105101 RELATED DB: TARGETTRACK
4hl2