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(-) Description

Title :  CTX-M-9 CLASS A BETA-LACTAMASE COMPLEXED WITH COMPOUND 3 (G30)
 
Authors :  Y. Chen, B. K. Shoichet
Date :  01 Feb 09  (Deposition) - 24 Mar 09  (Release) - 05 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Ctx-M, Beta-Lactamase, Molecular Docking, Fragment, Inhibitor, Antibiotic Resistance, Hydrolase, Plasmid, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Chen, B. K. Shoichet
Molecular Docking And Ligand Specificity In Fragment-Based Inhibitor Discovery
Nat. Chem. Biol. V. 5 358 2009
PubMed-ID: 19305397  |  Reference-DOI: 10.1038/NCHEMBIO.155
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE CTX-M-9A
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-9A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 29-291
    Gene: BLACTX-M-9, BLACTX-M-9A, CTX-M
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: BETA-LACTAMASE, CTX-M-9 BETA-LACTAMASE, BETALACTAMASE CTX-M-9

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1G303Ligand/Ion(1S,2R)-2-[(2,5-DIFLUOROPHENYL)CARBAMOYL]CYCLOPROPANECARBOXYLIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:70 , ASN A:104 , SER A:130 , ASN A:132 , ASN A:170 , SER A:237 , GLY A:238 , ASP A:240 , HOH A:309 , HOH A:311 , HOH A:347BINDING SITE FOR RESIDUE G30 A 1
2AC2SOFTWAREG30 A:3 , GLN A:83 , LEU A:142 , GLY A:146 , THR A:149 , ALA A:150 , ARG A:153 , HOH A:303 , HOH A:356 , HOH A:368 , HOH A:414BINDING SITE FOR RESIDUE G30 A 2
3AC3SOFTWAREG30 A:2 , ALA A:79 , LYS A:82 , GLN A:83 , ALA A:150 , PHE A:151 , ARG A:153 , ALA A:154 , HOH A:367 , HOH A:420BINDING SITE FOR RESIDUE G30 A 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G30)

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G30)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G30)

(-) Exons   (0, 0)

(no "Exon" information available for 3G30)

(-) 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:262
 aligned with Q9L5C8_ECOLX | Q9L5C8 from UniProtKB/TrEMBL  Length:291

    Alignment length:262
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289  
         Q9L5C8_ECOLX    30 TSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 291
               SCOP domains d3g30a_ A: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3g30A00 A:26-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.eeeeeeee....eeeee.....ee.hhhhhhhhhhhhhhhhh...hhhh.eeeehhhhh.....hhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g30 A  26 TSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 290
                                    35        45        55 ||     66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236 ||    247    || 258       268       278       288  
                                                          57|                                                                                                                                                                                238|         252|                                    
                                                           59                                                                                                                                                                                 240          254
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G30)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9L5C8_ECOLX | Q9L5C8)
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/TrEMBL
        Q9L5C8_ECOLX | Q9L5C8: 1ylj 1ym1 1yms 1ymx 2p74 3g2y 3g2z 3g31 3g32 3g34 3g35 3hlw 3hre 3huo 3hvf 3q07 3q1f 4dds 4ddy 4de0 4de1 4de2 4de3 4len 5ujo

(-) Related Entries Specified in the PDB File

3g2y 3g2z 3g31 3g32 3g34 3g35