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(-) Description

Title :  CTX-M-9 CLASS A BETA-LACTAMASE COMPLEXED WITH COMPOUND 4
 
Authors :  D. A. Nichols, Y. Chen
Date :  19 Jan 12  (Deposition) - 28 Mar 12  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.44
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ctx-M, Beta-Lactamase, Molecular Docking, Fragment, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Nichols, P. Jaishankar, W. Larson, E. Smith, G. Liu, R. Beyrouthy R. Bonnet, A. R. Renslo, Y. Chen
Structure-Based Design Of Potent And Ligand-Efficient Inhibitors Of Ctx-M Class A Beta-Lactamase
J. Med. Chem. V. 55 2163 2012
PubMed-ID: 22296601  |  Reference-DOI: 10.1021/JM2014138

(-) 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: UNP RESIDUES 29-291
    Gene: BLACTX-M-9, BLACTX-M-9A, BLACTX-M-9B, CTX-M
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    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  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1DMS2Ligand/IonDIMETHYL SULFOXIDE
2DN811Ligand/Ion3-BROMO-N-[3-(1H-TETRAZOL-5-YL)PHENYL]BENZAMIDE
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2DN86Ligand/Ion3-BROMO-N-[3-(1H-TETRAZOL-5-YL)PHENYL]BENZAMIDE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2DN85Ligand/Ion3-BROMO-N-[3-(1H-TETRAZOL-5-YL)PHENYL]BENZAMIDE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:104 , SER A:130 , ASN A:132 , PRO A:167 , ASN A:170 , THR A:235 , GLY A:236 , SER A:237 , GLY A:238 , ASP A:240 , DN8 A:302 , HOH A:417 , HOH A:445BINDING SITE FOR RESIDUE DN8 A 301
02AC2SOFTWAREASN A:104 , TYR A:105 , SER A:237 , DN8 A:301 , DN8 A:306 , HOH A:467 , HOH A:537BINDING SITE FOR RESIDUE DN8 A 302
03AC3SOFTWAREALA A:79 , ALA A:150 , PHE A:151 , ALA A:154 , HOH A:583BINDING SITE FOR RESIDUE DN8 A 303
04AC4SOFTWARETHR A:55 , ASP A:176 , THR B:86 , GLN B:87 , LYS B:88 , GLN B:89 , LEU B:90BINDING SITE FOR RESIDUE DN8 A 304
05AC5SOFTWAREASN A:54 , GLN A:188 , ARG A:191 , GLN A:192 , GLY A:196 , GLN B:83 , DN8 B:303 , HOH B:481 , HOH B:493 , HOH B:539BINDING SITE FOR RESIDUE DN8 A 305
06AC6SOFTWARESER A:274 , ARG A:276 , DN8 A:302 , HOH A:417BINDING SITE FOR RESIDUE DN8 A 306
07AC7SOFTWAREGLU A:37 , ARG A:61 , GLN B:56 , ARG B:184BINDING SITE FOR RESIDUE DMS A 307
08AC8SOFTWAREASN B:104 , SER B:130 , ASN B:132 , PRO B:167 , ASN B:170 , THR B:235 , GLY B:236 , SER B:237 , ASP B:240 , DN8 B:302 , HOH B:416 , HOH B:422BINDING SITE FOR RESIDUE DN8 B 301
09AC9SOFTWAREASN B:104 , TYR B:105 , SER B:237 , DN8 B:301 , HOH B:416 , HOH B:565 , HOH B:589BINDING SITE FOR RESIDUE DN8 B 302
10BC1SOFTWAREGLN A:192 , HIS A:197 , DN8 A:305 , HOH A:503 , HOH A:513 , ALA B:79 , LEU B:142 , GLY B:143 , PHE B:151 , DN8 B:304 , HOH B:493 , HOH B:525BINDING SITE FOR RESIDUE DN8 B 303
11BC2SOFTWAREHIS A:197 , GLY B:147 , ALA B:150 , ARG B:153 , DN8 B:303 , HOH B:486 , HOH B:525 , HOH B:543 , HOH B:612BINDING SITE FOR RESIDUE DN8 B 304
12BC3SOFTWAREILE B:108 , LYS B:111 , HIS B:112 , GLU B:121BINDING SITE FOR RESIDUE DN8 B 305
13BC4SOFTWAREGLY B:42 , ARG B:61BINDING SITE FOR RESIDUE DMS B 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DE3)

(-) 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 4DE3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DE3)

(-) Exons   (0, 0)

(no "Exon" information available for 4DE3)

(-) 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:260
 aligned with Q9L5C8_ECOLX | Q9L5C8 from UniProtKB/TrEMBL  Length:291

    Alignment length:260
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
         Q9L5C8_ECOLX    32 AVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 291
               SCOP domains d4de3a_ A: automated matches                                                                                                                                                                                                                                         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....eeeeeeee.....eeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4de3 A  28 AVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 290
                                    37        47        57|       68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238|      249  ||   260       270       280       290
                                                        57|                                                                                                                                                                                238|         252|                                    
                                                         59                                                                                                                                                                                 240          254                                    


Chain B from PDB  Type:PROTEIN  Length:261
 aligned with Q9L5C8_ECOLX | Q9L5C8 from UniProtKB/TrEMBL  Length:291

    Alignment length:261
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 
         Q9L5C8_ECOLX    31 SAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 291
               SCOP domains d4de3b_ B: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhhhh.hhhh.eeeehhhhh.....hhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh.....eeeeeeee...eeeeeeee.......eeeeeeee........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4de3 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)
  - → 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  (0, 0)

(no "CATH Domain" information available for 4DE3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DE3)

(-) 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 3g32 3g34 3g35 3hlw 3hre 3huo 3hvf 3q07 3q1f 4dds 4ddy 4de0 4de1 4de2 4len 5ujo

(-) Related Entries Specified in the PDB File

3g2y 3g2z 3g30 3g31 3g32 3g35 4dds 4ddy 4de0 4de1 4de2