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(-) Description

Title :  NEW DELHI METALLO-BETA-LACTAMASE-1 1.05 A STRUCTURE COMPLEXED WITH HYDROLYZED 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 :  1.05
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
New Delhi Metallo-Beta-Lactamase-1 1. 05 A Structure Complexed With Hydrolyzed 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, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2ZN5Ligand/IonZINC 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 (2, 5)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC 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 (2, 4)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC 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 (2, 9)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC 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  (14, 14)

Asymmetric Unit (14, 14)
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 , ZN A:302 , ZN A:303 , HOH A:416 , HOH A:458 , HOH A:701 , THR B:34 , PRO B:68 , GLY B:69BINDING SITE FOR RESIDUE ZZ7 A 301
02AC2SOFTWAREHIS A:120 , HIS A:122 , HIS A:189 , ZZ7 A:301 , HOH A:701BINDING SITE FOR RESIDUE ZN A 302
03AC3SOFTWAREASP A:124 , CYS A:208 , HIS A:250 , ZZ7 A:301 , HOH A:701BINDING SITE FOR RESIDUE ZN A 303
04AC4SOFTWAREPRO A:112 , VAL A:113 , EDO A:305 , HOH A:460BINDING SITE FOR RESIDUE EDO A 304
05AC5SOFTWAREASN A:57 , LYS A:106 , PRO A:112 , GLY A:200 , EDO A:304 , HOH A:424 , HOH A:499 , HOH A:560 , HOH A:682BINDING SITE FOR RESIDUE EDO A 305
06AC6SOFTWAREASP A:82 , ALA A:134 , ALA A:135 , HOH A:628BINDING SITE FOR RESIDUE EDO A 306
07AC7SOFTWAREARG A:234 , HOH A:472 , HOH A:488 , EDO B:306 , HOH B:518BINDING SITE FOR RESIDUE EDO A 307
08AC8SOFTWAREASP A:223 , ALA A:224 , HOH A:426 , ALA B:224 , ASP B:225 , HOH B:436 , HOH B:614BINDING SITE FOR RESIDUE EDO B 301
09AC9SOFTWARETHR 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 , ZN B:303 , ZN B:304 , HOH B:410 , HOH B:431 , HOH B:461 , HOH B:589 , HOH B:600 , HOH B:687BINDING SITE FOR RESIDUE ZZ7 B 302
10BC1SOFTWAREHIS B:120 , HIS B:122 , HIS B:189 , ZZ7 B:302 , HOH B:687BINDING SITE FOR RESIDUE ZN B 303
11BC2SOFTWAREASP B:124 , CYS B:208 , HIS B:250 , ZZ7 B:302 , HOH B:687BINDING SITE FOR RESIDUE ZN B 304
12BC3SOFTWAREGLU A:227 , GLU B:152 , ASP B:223 , HOH B:688BINDING SITE FOR RESIDUE ZN B 305
13BC4SOFTWAREARG A:234 , ASP A:267 , EDO A:307 , HOH A:521 , ARG B:234 , ALA B:235 , ALA B:238 , HOH B:427 , HOH B:428BINDING SITE FOR RESIDUE EDO B 306
14BC5SOFTWAREGLY A:71 , HOH A:503 , HOH A:698 , ASN B:220 , LEU B:221 , GLY B:222 , HOH B:670BINDING SITE FOR RESIDUE EDO B 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HL2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HL2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HL2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HL2)

(-) Exons   (0, 0)

(no "Exon" information available for 4HL2)

(-) 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:243
                                                                                                                                                                                                                                                                                   
               SCOP domains d4hl2a_ A: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeee..eeeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhh......eee........hhhhh.....eeee...........eeee....eee......................hhhhhhhhhhhhh....eee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hl2 A  28 SNAIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267   


Chain B from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains d4hl2b_ 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
                 4hl2 B  29 NAIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268
   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 4HL2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HL2)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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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 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
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