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(-) Description

Title :  1,2,4-TRIAZOLE-3-THIONE COMPOUNDS AS INHIBITORS OF L1, DI-ZINC METALLO-BETA-LACTAMASES.
 
Authors :  L. Nauton, G. Garau, R. Khan, O. Dideberg
Date :  14 Sep 15  (Deposition) - 11 Jan 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Hydrolase, Metallo, Zn, Lactamase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Sevaille, L. Gavara, C. Bebrone, F. De Luca, L. Nauton, M. Achard, P. Mercuri, S. Tanfoni, L. Borgianni, C. Guyon, P. Lonjon, G. Turan-Zitouni, J. Dzieciolowski, K. Becker, L. Benard, C. Condon, L. Maillard, J. Martinez, J. M. Frere, O. Dideberg, M. Galleni, J. D. Docquier, J. F. Hernandez
1, 2, 4-Triazole-3-Thione Compounds As Inhibitors Of Dizinc Metallo-Beta-Lactamases.
Chemmedchem V. 12 972 2017
PubMed-ID: 28505394  |  Reference-DOI: 10.1002/CMDC.201700186
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METALLO-BETA-LACTAMASE L1 TYPE 3
    Cellular Location: PERIPLASM
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector: PET26
    Expression System Vector Type: PLASMID
    Organism Common: PSEUDOMONAS MALTOPHILIA
    Organism Scientific: STENOTROPHOMONAS MALTOPHILIA
    Organism Taxid: 40324
    Synonym: B3 METALLO-BETA-LACTAMASE,BETA-LACTAMASE TYPE III,METALLO- BETA-LACTAMASE L1 TYPE III,PENICILLINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1L3B2Ligand/Ion5-(2-METHYLPHENYL)-3H-1,2,4-TRIAZOLE-3-THIONE
2SO44Ligand/IonSULFATE ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1L3B4Ligand/Ion5-(2-METHYLPHENYL)-3H-1,2,4-TRIAZOLE-3-THIONE
2SO48Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:105 , HIS A:107 , HIS A:181 , L3B A:403binding site for residue ZN A 401
02AC2SOFTWAREASP A:109 , HIS A:110 , HIS A:246 , L3B A:403binding site for residue ZN A 402
03AC3SOFTWARETYR A:32 , HIS A:107 , ASP A:109 , HIS A:110 , ASP A:142 , PHE A:145 , ILE A:149 , HIS A:181 , SER A:206 , TYR A:212 , HIS A:246 , ZN A:401 , ZN A:402 , HOH A:542 , HOH A:582binding site for residue L3B A 403
04AC4SOFTWAREALA A:258 , ARG A:259 , ALA A:260 , GLY A:261 , ALA A:262 , HOH A:559 , HOH A:563 , ARG B:235 , LYS B:268binding site for residue SO4 A 404
05AC5SOFTWAREARG A:158 , ILE A:166 , THR A:167 , HOH A:575binding site for residue SO4 A 405
06AC6SOFTWARETRP A:52 , ARG A:91 , HOH A:515 , HOH A:553binding site for residue SO4 A 406
07AC7SOFTWAREHIS B:105 , HIS B:107 , HIS B:181 , L3B B:403binding site for residue ZN B 401
08AC8SOFTWAREASP B:109 , HIS B:110 , HIS B:246 , L3B B:403binding site for residue ZN B 402
09AC9SOFTWARETYR B:32 , HIS B:105 , HIS B:107 , ASP B:109 , HIS B:110 , PHE B:145 , ILE B:149 , HIS B:181 , SER B:206 , TYR B:212 , HIS B:246 , ZN B:401 , ZN B:402 , HOH B:505binding site for residue L3B B 403
10AD1SOFTWAREARG B:158 , ILE B:166 , THR B:167 , HOH B:538 , HOH B:612 , HOH B:644binding site for residue SO4 B 404

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:239 -A:267
2B:239 -B:267

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DPX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DPX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DPX)

(-) Exons   (0, 0)

(no "Exon" information available for 5DPX)

(-) 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:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhh....eeee..eee........eeeee..eeeee...hhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhh..eeeehhhhhhhhhh....................ee.....eeee..eeeeeee........eeeeeeeee..eeeeeee..................hhhhhhhhhhhhhhhh...eee..hhhhhh....hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dpx A  23 EVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 288
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      


Chain B from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhh....ee....eee........eeeee..eeeee...hhhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhh..eeeehhhhhhhhhh....................ee.....eeee..eeeeeee........eeeeeeeee..eeeeeee..................hhhhhhhhhhhhhhh....eee..hhhhhh....hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dpx B  23 EVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 288
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 5DPX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DPX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DPX)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BLA1_STEMA | P52700: 1sml 2aio 2fm6 2fu6 2fu7 2fu8 2fu9 2gfj 2gfk 2h6a 2hb9 2qdt 2qin 2qjs 5evb 5evd 5evk 5hh5 5hh6

(-) Related Entries Specified in the PDB File

2fm6 NATIVE FORM
2fu7 CU-SUBSTITUTED FORM
2fu8 D-CAPTOPRIL COMPLEX
2fu9 MP2 INHIBITOR COMPLEX
2gfj INHIBITOR 1 COMPLEX
2gfk INHIBITOR 2 COMPLEX
2hb9 INHIBITOR 3 COMPLEX