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(-) Description

Title :  CTX-M-9 CLASS A BETA-LACTAMASE COMPLEXED WITH COMPOUND 6 (3G3)
 
Authors :  Y. Chen, B. K. Shoichet
Date :  01 Feb 09  (Deposition) - 24 Mar 09  (Release) - 05 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.31
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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, B
    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

  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  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
13G33Ligand/Ion2-[2-(1H-TETRAZOL-5-YL)ETHYL]-1H-ISOINDOLE-1,3(2H)-DIONE
2DMS6Ligand/IonDIMETHYL SULFOXIDE
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
13G31Ligand/Ion2-[2-(1H-TETRAZOL-5-YL)ETHYL]-1H-ISOINDOLE-1,3(2H)-DIONE
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
13G32Ligand/Ion2-[2-(1H-TETRAZOL-5-YL)ETHYL]-1H-ISOINDOLE-1,3(2H)-DIONE
2DMS4Ligand/IonDIMETHYL SULFOXIDE
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREDMS A:10 , SER A:70 , TYR A:105 , SER A:130 , ASN A:132 , THR A:235 , GLY A:236 , SER A:237 , HOH A:379 , HOH A:430 , HOH A:483 , HOH A:569BINDING SITE FOR RESIDUE 3G3 A 1
02AC2SOFTWAREARG A:222 , PRO A:226 , THR A:227 , TRP A:229 , HOH A:559BINDING SITE FOR RESIDUE DMS A 9
03AC3SOFTWARE3G3 A:1 , TYR A:105 , THR A:216 , HOH A:557 , HOH A:563BINDING SITE FOR RESIDUE DMS A 10
04AC4SOFTWAREPO4 B:4 , SER B:70 , ASN B:104 , TYR B:105 , SER B:130 , ASN B:132 , THR B:235 , GLY B:236 , SER B:237 , HOH B:353 , HOH B:370 , HOH B:413 , HOH B:571 , HOH B:572 , HOH B:584BINDING SITE FOR RESIDUE 3G3 B 2
05AC5SOFTWARELYS A:38 , ALA A:150 , HOH A:544 , DMS B:5 , DMS B:8 , ASN B:54 , GLN B:188 , ARG B:191 , GLY B:196 , HOH B:406BINDING SITE FOR RESIDUE 3G3 B 3
06AC6SOFTWARE3G3 B:2 , SER B:70 , SER B:130 , THR B:235 , GLY B:236 , SER B:237 , HOH B:353 , HOH B:370 , HOH B:401 , HOH B:571 , HOH B:584BINDING SITE FOR RESIDUE PO4 B 4
07AC7SOFTWAREARG A:61 , HOH A:513 , 3G3 B:3 , ILE B:49 , ASN B:54 , GLN B:56 , ARG B:191 , HOH B:557BINDING SITE FOR RESIDUE DMS B 5
08AC8SOFTWAREGLU A:37 , ARG A:61 , GLN B:56 , ARG B:184BINDING SITE FOR RESIDUE DMS B 6
09AC9SOFTWAREARG B:222 , PRO B:226 , THR B:227 , TRP B:229 , HOH B:345BINDING SITE FOR RESIDUE DMS B 7
10BC1SOFTWAREGLY A:143 , GLY A:147 , 3G3 B:3 , GLN B:192 , ALA B:198 , HOH B:406BINDING SITE FOR RESIDUE DMS B 8

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G32)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:166 -Pro A:167
2Glu B:166 -Pro B:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G32)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G32)

(-) Exons   (0, 0)

(no "Exon" information available for 3G32)

(-) 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: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 d3g32a_ A: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3g32A00 A:26-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.eeeeeeee.....eeee.....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
                 3g32 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                                    


Chain B 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 d3g32b_ B: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3g32B00 B:26-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.eeeeeeee.....eeee.....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
                 3g32 B  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)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G32)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  3.5.2.6
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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 3g30 3g31 3g34 3g35 3hlw 3hre 3huo 3hvf 3q07 3q1f 4dds 4ddy 4de0 4de1 4de2 4de3 4len 5ujo

(-) Related Entries Specified in the PDB File

3g2y 3g30 3g31 3g33 3g34 3g35 3g3z