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(-) Description

Title :  NEW DELHI METALLO-BETA-LACTAMASE-1 COMPLEXED WITH CD
 
Authors :  Y. Kim, C. Tesar, R. Jedrzejczak, J. Babnigg, T. A. Binkowski, J. Mire, J. Sacchettini, A. Joachimiak, Midwest Center For Structural Ge (Mcsg), Structures Of Mtb Proteins Conferring Susceptibility Mtb Inhibitors (Mtbi)
Date :  07 Jul 11  (Deposition) - 20 Jul 11  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Alpha-Beta Sandwich, Hydrolase, Structures Of Mtb Proteins Conferring Susceptibility To Known Mtb Inhibitors, Mtbi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, C. Tesar, R. Jedrzejczak, J. Babnigg, T. A. Binkowski, J. Mire, J. Sacchettini, A. Joachimiak
New Delhi Metallo-Beta-Lactamase-1 Complexed With Cd
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
    Fragment: SEQUENCE DATABASE RESIDUES 37-270
    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  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1CD6Ligand/IonCADMIUM ION
2CL4Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4SCN-1Ligand/IonTHIOCYANATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4SCN1Ligand/IonTHIOCYANATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:124 , CYS A:208 , HIS A:250 , CD A:281 , CL A:284 , CL A:285BINDING SITE FOR RESIDUE CD A 280
02AC2SOFTWAREHIS A:120 , HIS A:122 , ASP A:124 , HIS A:189 , CYS A:208 , CD A:280 , CL A:285BINDING SITE FOR RESIDUE CD A 281
03AC3SOFTWAREGLU A:152 , ASP A:223 , GLU A:227 , HOH A:320BINDING SITE FOR RESIDUE CD A 282
04AC4SOFTWAREASP A:199 , ASP A:202 , ILE A:203 , PHE A:240 , PRO A:241 , LYS A:242 , ALA A:243 , ASN B:166BINDING SITE FOR RESIDUE GOL A 283
05AC5SOFTWAREHIS A:189 , LYS A:211 , ASN A:220 , HIS A:250 , CD A:280 , CL A:285 , GLY B:69BINDING SITE FOR RESIDUE CL A 284
06AC6SOFTWAREHIS A:122 , ASP A:124 , HIS A:189 , ASN A:220 , CD A:280 , CD A:281 , CL A:284 , PRO B:68BINDING SITE FOR RESIDUE CL A 285
07AC7SOFTWARETRP A:168 , HOH A:305 , LYS B:181BINDING SITE FOR RESIDUE GOL A 271
08AC8SOFTWAREALA B:164 , ASN B:166BINDING SITE FOR RESIDUE SCN B 286
09AC9SOFTWAREHIS B:120 , HIS B:122 , ASP B:124 , HIS B:189 , CYS B:208 , CL B:271 , CD B:281BINDING SITE FOR RESIDUE CD B 280
10BC1SOFTWAREASP B:124 , CYS B:208 , HIS B:250 , CL B:271 , CD B:280 , CL B:285BINDING SITE FOR RESIDUE CD B 281
11BC2SOFTWAREGLU B:152 , ASP B:223 , HOH B:277 , HOH B:292BINDING SITE FOR RESIDUE CD B 282
12BC3SOFTWARELYS B:181 , ILE B:198 , PHE B:240 , PRO B:241 , LYS B:242 , ALA B:243BINDING SITE FOR RESIDUE GOL B 284
13BC4SOFTWAREGLY A:69 , HIS B:189 , LYS B:211 , ASN B:220 , HIS B:250 , CL B:271 , CD B:281BINDING SITE FOR RESIDUE CL B 285
14BC5SOFTWAREHIS B:122 , ASP B:124 , HIS B:189 , ASN B:220 , CD B:280 , CD B:281 , CL B:285BINDING SITE FOR RESIDUE CL B 271

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SRX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SRX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SRX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SRX)

(-) Exons   (0, 0)

(no "Exon" information available for 3SRX)

(-) 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:237
 aligned with BLAN1_KLEPN | C7C422 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:237
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       
          BLAN1_KLEPN    34 TIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
               SCOP domains d3srxa_ 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..................eeee...........eeee....eeeee....................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3srx A  34 SNANYMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       


Chain B from PDB  Type:PROTEIN  Length:229
 aligned with BLAN1_KLEPN | C7C422 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:229
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261         
          BLAN1_KLEPN    42 GDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
               SCOP domains d3srxb_ B: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhh...eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eeeee....................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3srx B  42 GDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261
   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 3SRX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SRX)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BLAN1_KLEPN | C7C422)
molecular function
    GO:0008800    beta-lactamase activity    Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0017001    antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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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 3zr9 4exs 4exy 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

3rkj DIFFERENT CONSTRUCT THE SAME PROTEIN, DELTA-38
3rkk THE SAME CONSTRUCT, DELTA-36NY WITHOUT METAL BOUND
3sbl THE SAME CONSTRUCT, DELTA-36NY, DIFFERENT CRYSTAL FORM
3sfp DELTA-36NY CONSTRUCT, SINGLE ZN-BOUND FORM RELATED ID: APC105101 RELATED DB: TARGETDB