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(-) Description

Title :  NEW DELHI METALLO-BETA-LACTAMASE-1, COMPLEXED WITH CD AND FAROPENEM
 
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) - 23 Jan 13  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Structures Of Mtb Proteins Conferring Susceptibility To Known Mtb Inhibitors, Mtbi, Alpha-Beta- Beta-Alpha Sandwich, Hydrolase, Psi-Biology, 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, Complexed With Cd And Faropenem
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  (5, 16)

Asymmetric Unit (5, 16)
No.NameCountTypeFull Name
1CD6Ligand/IonCADMIUM ION
2CL4Ligand/IonCHLORIDE ION
3FPM2Ligand/Ion(5R,6S)-6-(1-HYDROXYETHYL)-7-OXO-3-[(2R)-OXOLAN-2-YL]-4-THIA-1-AZABICYCLO[3.2.0]HEPT-2-ENE-2-CARBOXYLIC ACID
4GOL2Ligand/IonGLYCEROL
5SFR2Ligand/Ion(2R)-2-[(1S,2R)-1-CARBOXY-2-HYDROXYPROPYL]-5-[(2R)-OXOLAN-2-YL]-2,3-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLICACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3FPM1Ligand/Ion(5R,6S)-6-(1-HYDROXYETHYL)-7-OXO-3-[(2R)-OXOLAN-2-YL]-4-THIA-1-AZABICYCLO[3.2.0]HEPT-2-ENE-2-CARBOXYLIC ACID
4GOL-1Ligand/IonGLYCEROL
5SFR1Ligand/Ion(2R)-2-[(1S,2R)-1-CARBOXY-2-HYDROXYPROPYL]-5-[(2R)-OXOLAN-2-YL]-2,3-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLICACID
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3FPM1Ligand/Ion(5R,6S)-6-(1-HYDROXYETHYL)-7-OXO-3-[(2R)-OXOLAN-2-YL]-4-THIA-1-AZABICYCLO[3.2.0]HEPT-2-ENE-2-CARBOXYLIC ACID
4GOL2Ligand/IonGLYCEROL
5SFR1Ligand/Ion(2R)-2-[(1S,2R)-1-CARBOXY-2-HYDROXYPROPYL]-5-[(2R)-OXOLAN-2-YL]-2,3-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLICACID
Biological Unit 3 (3, 6)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3FPM2Ligand/Ion(5R,6S)-6-(1-HYDROXYETHYL)-7-OXO-3-[(2R)-OXOLAN-2-YL]-4-THIA-1-AZABICYCLO[3.2.0]HEPT-2-ENE-2-CARBOXYLIC ACID
4GOL2Ligand/IonGLYCEROL
5SFR2Ligand/Ion(2R)-2-[(1S,2R)-1-CARBOXY-2-HYDROXYPROPYL]-5-[(2R)-OXOLAN-2-YL]-2,3-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLICACID

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:93 , HIS A:122 , ASP A:124 , HIS A:189 , CYS A:208 , LYS A:211 , ASN A:220 , HIS A:250 , CD A:303 , CD A:304 , HOH A:417BINDING SITE FOR RESIDUE FPM A 301
02AC2SOFTWARETRP A:93 , HIS A:122 , ASP A:124 , LYS A:211 , GLY A:219 , ASN A:220 , HIS A:250 , CD A:303 , CD A:304BINDING SITE FOR RESIDUE SFR A 302
03AC3SOFTWAREHIS A:120 , HIS A:122 , HIS A:189 , CYS A:208 , FPM A:301 , SFR A:302 , CD A:304BINDING SITE FOR RESIDUE CD A 303
04AC4SOFTWAREASP A:124 , CYS A:208 , HIS A:250 , FPM A:301 , SFR A:302 , CD A:303BINDING SITE FOR RESIDUE CD A 304
05AC5SOFTWAREGLU A:152 , ASP A:223 , HOH A:431 , GLU B:227BINDING SITE FOR RESIDUE CD A 305
06AC6SOFTWAREPHE A:240 , PRO A:241 , LYS A:242 , ALA A:243BINDING SITE FOR RESIDUE CL A 306
07AC7SOFTWARELYS A:216BINDING SITE FOR RESIDUE CL A 307
08AC8SOFTWAREGLY B:69 , PHE B:70 , HIS B:122 , ASP B:124 , HIS B:189 , LYS B:211 , GLY B:219 , ASN B:220 , HIS B:250 , CD B:305 , CD B:306BINDING SITE FOR RESIDUE SFR B 301
09AC9SOFTWAREGLY B:69 , PHE B:70 , TRP B:93 , HIS B:122 , ASP B:124 , HIS B:189 , LYS B:211 , GLY B:219 , ASN B:220 , HIS B:250 , CD B:305 , CD B:306BINDING SITE FOR RESIDUE FPM B 302
10BC1SOFTWAREARG B:32BINDING SITE FOR RESIDUE GOL B 303
11BC2SOFTWAREASP A:48 , ARG B:32 , ARG B:45 , HOH B:487BINDING SITE FOR RESIDUE GOL B 304
12BC3SOFTWAREHIS B:120 , HIS B:122 , ASP B:124 , HIS B:189 , CYS B:208 , SFR B:301 , FPM B:302 , CD B:306BINDING SITE FOR RESIDUE CD B 305
13BC4SOFTWAREASP B:124 , CYS B:208 , HIS B:250 , SFR B:301 , FPM B:302 , CD B:305BINDING SITE FOR RESIDUE CD B 306
14BC5SOFTWAREGLU A:227 , GLU B:152 , ASP B:223 , HOH B:465BINDING SITE FOR RESIDUE CD B 307
15BC6SOFTWAREPHE B:240 , PRO B:241 , LYS B:242 , ALA B:243 , HOH B:475BINDING SITE FOR RESIDUE CL B 308
16BC7SOFTWARELYS B:216BINDING SITE FOR RESIDUE CL B 309

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HKY)

(-) 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:228
                                                                                                                                                                                                                                                                    
               SCOP domains d4hkya_ A: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeee..eeeeeeeee...eeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhh.........eee........hhhhh.....eeee...........eeee....eeeee.................hhhhhhhhhhhhhhhh....eeee..eeee.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hky A  41 TGDQRFGDLVFRQLAPNVWQHTSYLDMPGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    50        60       |72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262        
                                                      68|                                                                                                                                                                                                       
                                                       71                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains d4hkyb_ B: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh....eee..eeeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhh.........eee........hhhhh.....eeee...........eeee....eeeee....................hhhhhhhhhhhhh....eeee..eeee.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hky 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 4HKY)

(-) Pfam Domains  (0, 0)

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

(-) 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 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
4h0d NDM1, DELTA-30 CONSTRUCT, TWO CD-BOUND AND PARTIAL FAROPENEM RELATED ID: MCSG-APC105101 RELATED DB: TARGETTRACK
4hl1
4hl2