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(-) Description

Title :  CTX-M-9 CLASS A BETA-LACTAMASE COMPLEXED WITH COMPOUND 10
 
Authors :  D. A. Nichols, Y. Chen
Date :  19 Jan 12  (Deposition) - 28 Mar 12  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.36
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ctx-M, Molecular Docking, Fragment, Inhibitor, 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, 15)

Asymmetric Unit (2, 15)
No.NameCountTypeFull Name
1DMS3Ligand/IonDIMETHYL SULFOXIDE
2DN612Ligand/IonN-[3-(1H-TETRAZOL-5-YL)PHENYL]-3-(TRIFLUOROMETHYL)BENZAMIDE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1DMS2Ligand/IonDIMETHYL SULFOXIDE
2DN64Ligand/IonN-[3-(1H-TETRAZOL-5-YL)PHENYL]-3-(TRIFLUOROMETHYL)BENZAMIDE
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2DN68Ligand/IonN-[3-(1H-TETRAZOL-5-YL)PHENYL]-3-(TRIFLUOROMETHYL)BENZAMIDE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:104 , TYR A:105 , SER A:130 , ASN A:132 , PRO A:167 , THR A:168 , ASN A:170 , THR A:171 , THR A:235 , GLY A:236 , SER A:237 , ASP A:240 , ARG A:256 , DN6 A:302 , HOH A:412 , HOH A:415BINDING SITE FOR RESIDUE DN6 A 301
02AC2SOFTWAREASN A:104 , TYR A:105 , SER A:130 , THR A:216 , SER A:237 , DN6 A:301 , HOH A:508BINDING SITE FOR RESIDUE DN6 A 302
03AC3SOFTWARETHR A:51 , ALA A:52 , ASN A:54 , ARG A:191 , GLN A:192 , GLY A:196 , DN6 A:304 , HOH A:452 , HOH A:496 , HOH A:545 , HOH A:558 , HOH A:589 , HOH B:520BINDING SITE FOR RESIDUE DN6 A 303
04AC4SOFTWAREASN A:54 , HIS A:197 , DN6 A:303 , HOH A:558 , HOH A:624 , LYS B:82 , GLN B:83 , LEU B:142 , GLY B:147 , ALA B:150 , ALA B:154 , HOH B:464 , HOH B:509 , HOH B:520 , HOH B:579 , HOH B:597BINDING SITE FOR RESIDUE DN6 A 304
05AC5SOFTWAREGLU A:37 , ARG A:61 , GLN B:56 , ARG B:184 , HOH B:617BINDING SITE FOR RESIDUE DMS A 305
06AC6SOFTWAREGLN A:188 , ALA B:140 , GLN B:141BINDING SITE FOR RESIDUE DMS A 306
07AC7SOFTWAREILE B:108 , LYS B:111 , HIS B:112 , GLU B:121 , ALA B:124 , ALA B:125 , GLN B:128 , TYR B:129 , HOH B:596BINDING SITE FOR RESIDUE DN6 B 301
08AC8SOFTWAREASN B:104 , TYR B:105 , SER B:130 , THR B:216 , SER B:237 , DN6 B:303 , DN6 B:308 , HOH B:456BINDING SITE FOR RESIDUE DN6 B 302
09AC9SOFTWAREASN B:104 , TYR B:105 , SER B:130 , ASN B:132 , PRO B:167 , THR B:168 , ASN B:170 , THR B:171 , THR B:235 , GLY B:236 , SER B:237 , ASP B:240 , ARG B:256 , DN6 B:302 , HOH B:420 , HOH B:432BINDING SITE FOR RESIDUE DN6 B 303
10BC1SOFTWAREARG A:184 , GLN B:89 , ASN B:92 , GLN B:93 , PRO B:94 , TYR B:241 , GLN B:270 , HOH B:543 , HOH B:553 , HOH B:558 , HOH B:618BINDING SITE FOR RESIDUE DN6 B 304
11BC2SOFTWAREILE A:173 , HOH A:595 , ARG B:65 , ILE B:173 , PRO B:174 , GLY B:175 , ASP B:176 , DN6 B:306 , HOH B:483BINDING SITE FOR RESIDUE DN6 B 305
12BC3SOFTWAREILE A:173 , ASP A:176 , ARG A:178 , GLN B:87 , LYS B:88 , GLN B:89 , LEU B:90 , DN6 B:305 , HOH B:530 , HOH B:618BINDING SITE FOR RESIDUE DN6 B 306
13BC4SOFTWAREASP A:63 , HOH A:474 , HOH A:506 , HOH A:557 , GLN B:30 , GLN B:56 , LEU B:59 , TYR B:60 , ARG B:61 , GLY B:62 , HOH B:424 , HOH B:526BINDING SITE FOR RESIDUE DN6 B 307
14BC5SOFTWAREASN B:104 , TRP B:229 , GLN B:254 , ARG B:256 , LEU B:290 , DN6 B:302 , HOH B:630BINDING SITE FOR RESIDUE DN6 B 308
15BC6SOFTWAREALA B:218 , ARG B:222 , THR B:227 , HOH B:426 , HOH B:562BINDING SITE FOR RESIDUE DMS B 309

(-) SS Bonds  (0, 0)

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

(-) 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 4DDY)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DDY)

(-) 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 d4ddya_ A: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhh...hhhh.eeeehhhhh.....hhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ddy 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 d4ddyb_ B: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhh....hhhh.eeeehhhhh.....hhhhhh.eeeehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh.....eeeeeeee...eeeeeeee.......eeeeeeee........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ddy 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 4DDY)

(-) Pfam Domains  (0, 0)

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

(-) 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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 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 4de0 4de1 4de2 4de3 4len 5ujo

(-) Related Entries Specified in the PDB File

3g2y 3g2z 3g30 3g31 3g32 3g35 4dds 4de0 4de1 4de2 4de3 4de5