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(-) Description

Title :  NEW DELHI METALLO-BETA-LACTAMASE-1 COMPLEXED WITH MN FROM KLEBSIELLA PNEUMONIAE
 
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 Sep 12  (Deposition) - 26 Sep 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
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, Structures Of Mtb Proteins Conferring Susceptibility To Known Mtb Inhibitors, Mtbi, Alpha-Beta-Beta-Alpha Fold, Hydrolase, Hydrolase-Antibiotics Complex, Hydrolase-Antibiotic Complex (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 Mn From Klebsiella Pneumoniae
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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 12)

Asymmetric Unit (7, 12)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2FMT1Ligand/IonFORMIC ACID
3GOL1Ligand/IonGLYCEROL
4MN5Ligand/IonMANGANESE (II) ION
5NA1Ligand/IonSODIUM ION
6SO41Ligand/IonSULFATE ION
7ZZ72Ligand/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 (3, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2FMT-1Ligand/IonFORMIC ACID
3GOL1Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5NA-1Ligand/IonSODIUM ION
6SO4-1Ligand/IonSULFATE ION
7ZZ71Ligand/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 (3, 3)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2FMT1Ligand/IonFORMIC ACID
3GOL-1Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5NA-1Ligand/IonSODIUM ION
6SO41Ligand/IonSULFATE ION
7ZZ71Ligand/Ion(2R,4S)-2-[(R)-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}(CARBOXY)METHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU 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 , MN A:302 , MN A:303 , HOH A:402 , HOH A:436 , HOH A:455 , HOH A:518 , THR B:34 , GLY B:69BINDING SITE FOR RESIDUE ZZ7 A 301
02AC2SOFTWAREHIS A:120 , HIS A:122 , HIS A:189 , ZZ7 A:301 , HOH A:402BINDING SITE FOR RESIDUE MN A 302
03AC3SOFTWAREASP A:124 , CYS A:208 , HIS A:250 , ZZ7 A:301 , HOH A:402BINDING SITE FOR RESIDUE MN A 303
04AC4SOFTWAREPRO A:253 , SER A:255 , GOL A:305BINDING SITE FOR RESIDUE EDO A 304
05AC5SOFTWAREASP A:95 , ASP A:130 , EDO A:304 , HOH A:644BINDING SITE FOR RESIDUE GOL A 305
06AC6SOFTWAREGLU A:227 , HIS A:228 , HOH A:593 , GLU B:152 , ASP B:223 , FMT B:304 , HOH B:427BINDING SITE FOR RESIDUE MN A 306
07AC7SOFTWARETHR A:34 , PRO A:68 , 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 , MN B:302 , MN B:303 , HOH B:402 , HOH B:426 , HOH B:557BINDING SITE FOR RESIDUE ZZ7 B 301
08AC8SOFTWAREHIS B:120 , HIS B:122 , HIS B:189 , ZZ7 B:301 , HOH B:402BINDING SITE FOR RESIDUE MN B 302
09AC9SOFTWAREASP B:124 , CYS B:208 , HIS B:250 , ZZ7 B:301 , HOH B:402BINDING SITE FOR RESIDUE MN B 303
10BC1SOFTWAREGLU A:227 , MN A:306 , HIS B:122 , GLU B:152 , ASP B:223 , HOH B:503BINDING SITE FOR RESIDUE FMT B 304
11BC2SOFTWAREARG A:264 , LYS A:268 , ARG B:270BINDING SITE FOR RESIDUE SO4 B 305
12BC3SOFTWAREASP B:95 , ASP B:130 , HOH B:405 , HOH B:467 , HOH B:623BINDING SITE FOR RESIDUE NA B 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H0D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4H0D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H0D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H0D)

(-) Exons   (0, 0)

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(-) 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 d4h0da_ 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
                 4h0d A  30 AIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 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 d4h0db_ B: 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....eeeee....................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h0d B  30 AIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 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 4H0D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H0D)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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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 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 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 RELATED ID: MCSG-APC105101 RELATED DB: TARGETTRACK