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(-) Description

Title :  KPC-2 CARBAPENEMASE IN COMPLEX WITH 3-NPBA
 
Authors :  W. Ke, F. Van Den Akker
Date :  10 May 11  (Deposition) - 21 Mar 12  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.62
Chains :  Asym./Biol. Unit :  A
Keywords :  Inhibitor, Beta-Lactamase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Ke, C. R. Bethel, K. M. Papp-Wallace, S. R. Pagadala, M. Nottingham, D. Fernandez, J. D. Buynak, R. A. Bonomo, F. Van Den Akker
Crystal Structures Of Kpc-2 {Beta}-Lactamase In Complex Wit 3-Nitrophenyl Boronic Acid And The Penam Sulfone Psr-3-226.
Antimicrob. Agents Chemother. V. 56 2713 2012
PubMed-ID: 22330909  |  Reference-DOI: 10.1128/AAC.06099-11

(-) Compounds

Molecule 1 - CARBEPENEM-HYDROLYZING BETA-LACTAMASE KPC
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 26-289
    Gene: BLA, BLAKPC-2, KPC, KPC1
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573
    Synonym: KPC-1, KPC-2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NPB1Ligand/Ion3-NITROPHENYLBORONIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:69 , SER A:70 , TRP A:105 , SER A:130 , ASN A:132 , GLU A:166 , ASN A:170 , THR A:237 , ARG A:256BINDING SITE FOR RESIDUE NPB A 600

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:69 -A:238

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:166 -Leu A:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RXX)

(-) Sequences/Alignments

Asymmetric/Biological 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:263
 aligned with BLKPC_KLEPN | Q9F663 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:263
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286   
          BLKPC_KLEPN    27 NLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLG 289
               SCOP domains d3rxxa_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhhh........ee..hhhhh...hhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.hhhh.eeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rxx A  27 NLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLG 291
                                    36        46        56||      67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247    || 258       268       278       288   
                                                         57|                                                                                                                                                                                              252|                                     
                                                          59                                                                                                                                                                                               254
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RXX)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BLKPC_KLEPN | Q9F663)
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.
biological process
    GO:0030655    beta-lactam antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of a beta-lactam antibiotic, any member of a class of natural or semisynthetic antibiotics whose characteristic feature is a strained, four-membered beta-lactam ring. They include the penicillins and many of the cephalosporins.
    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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BLKPC_KLEPN | Q9F663: 2ov5 3e2k 3e2l 3rxw 4zbe 5eec 5uj3 5uj4 5ul8

(-) Related Entries Specified in the PDB File

3qxw THE SAME PROTEIN COMPLEXED WITH PSR3-226