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(-) Description

Title :  CTX-M-9 IN COMPLEX WITH THE BROAD SPECTRUM INHIBITOR 3-(2-CARBOXYVINYL)BENZO(B)THIOPHENE-2-BORONIC ACID
 
Authors :  D. Tondi
Date :  26 Jun 13  (Deposition) - 18 Jun 14  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Binding Sites, Structure Base Drug Design, Drug Discovery, Molecular, Enzyme Inhibitors, Beta Lactamases, Boronic Acids, Broad Spectrum, Bacterial Resistance, Double Perturbation Cycle Analysis, Thermodynamics, Structure Activity Relationship, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Tondi, A. Venturelli, R. Bonnet, C. Pozzi, B. K. Shoichet, M. P. Cost
Targeting Class A And C Serine Beta-Lactamases With A Broad-Spectrum Boronic Acid Derivative.
J. Med. Chem. V. 57 5449 2014
PubMed-ID: 24882105  |  Reference-DOI: 10.1021/JM5006572

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    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: 469008
    Expression System Vector Type: PLASMID
    Fragment: CTX-M9
    Gene: BLACTX-M-9, BLACTX-M-9A, BLACTX-M-9A BLACTX-M-9 BLACTX-M-9B, BLACTX-M-9B
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: K12
    Synonym: BETA-LACTAMASE CTX-M, BETA-LACTAMASE CTX-M-9A, BETALACTAMASE CTX-M-9, CTX-M-9 BETA-LACTAMASE, CTX-M-9 EXTENDED-SPECTRUM BETA- LACTAMASE

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
12GK2Ligand/Ion(2E)-3-[2-(DIHYDROXYBORANYL)-1-BENZOTHIOPHEN-3-YL]PROP-2-ENOIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
12GK1Ligand/Ion(2E)-3-[2-(DIHYDROXYBORANYL)-1-BENZOTHIOPHEN-3-YL]PROP-2-ENOIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12GK1Ligand/Ion(2E)-3-[2-(DIHYDROXYBORANYL)-1-BENZOTHIOPHEN-3-YL]PROP-2-ENOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:69 , SER A:70 , ASN A:104 , TYR A:105 , SER A:130 , ASN A:132 , GLU A:166 , ASN A:170 , THR A:235 , GLY A:236 , SER A:237 , HOH A:433 , HOH A:634BINDING SITE FOR RESIDUE 2GK A 300
2AC2SOFTWARECYS B:69 , SER B:70 , LYS B:73 , ASN B:104 , TYR B:105 , SER B:130 , ASN B:132 , GLU B:166 , ASN B:170 , THR B:216 , LYS B:234 , THR B:235 , GLY B:236 , SER B:237 , HOH B:614BINDING SITE FOR RESIDUE 2GK B 300

(-) SS Bonds  (0, 0)

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

(-) 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 4LEN)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LEN)

(-) 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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4len A  25 QTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 290
                                    34        44        54  ||    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246     ||257       267       277       287   
                                                           57|                                                                                                                                                                                238|         252|                                    
                                                            59                                                                                                                                                                                 240          254                                    


Chain B from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4len B  27 SAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 290
                                    36        46        56||      67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237||     248   ||  259       269       279       289 
                                                         57|                                                                                                                                                                                238|         252|                                    
                                                          59                                                                                                                                                                                 240          254
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4LEN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LEN)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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        Q9L5C8_ECOLX | Q9L5C8: 1ylj 1ym1 1yms 1ymx 2p74 3g2y 3g2z 3g30 3g31 3g32 3g34 3g35 3hlw 3hre 3huo 3hvf 3q07 3q1f 4dds 4ddy 4de0 4de1 4de2 4de3 5ujo

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