5DPX

1,2,4-Triazole-3-thione compounds as inhibitors of L1, di-zinc metallo-beta-lactamases.

> Summary

Summary for 5DPX

Related2FM6 2FU7 2FU8 2FU9 2GFJ 2GFK 2HB9
DescriptorMetallo-beta-lactamase L1 type 3, ZINC ION, 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione, ... (5 entities in total)
Functional Keywordshydrolase, metallo, zn, lactamase
Biological sourceStenotrophomonas maltophilia (Pseudomonas maltophilia)
Cellular locationPeriplasm  P52700
Total number of polymer chains2
Total molecular weight58505.27
Authors
Nauton, L.,Garau, G.,Khan, R.,Dideberg, O. (deposition date: 2015-09-14, release date: 2017-01-11, Last modification date: 2017-06-28)
Primary citation
Sevaille, L.,Gavara, L.,Bebrone, C.,De Luca, F.,Nauton, L.,Achard, M.,Mercuri, P.,Tanfoni, S.,Borgianni, L.,Guyon, C.,Lonjon, P.,Turan-Zitouni, G.,Dzieciolowski, J.,Becker, K.,Benard, L.,Condon, C.,Maillard, L.,Martinez, J.,Frere, J.M.,Dideberg, O.,Galleni, M.,Docquier, J.D.,Hernandez, J.F.
1,2,4-Triazole-3-thione Compounds as Inhibitors of Dizinc Metallo-beta-lactamases.
ChemMedChem, 12:972-985, 2017
PubMed: 28505394 (PDB entries with the same primary citation)
DOI: 10.1002/cmdc.201700186
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.85 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.208200.5%0.2%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5dpx
no rotation
Molmil generated image of 5dpx
rotated about x axis by 90°
Molmil generated image of 5dpx
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 5dpx
no rotation
Molmil generated image of 5dpx
rotated about x axis by 90°
Molmil generated image of 5dpx
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (5dpx.pdb1.gz [187.68 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BMetallo-beta-lactamase L1 type 3polymer26928740.52
UniProt (P52700)
Pfam (PF00753)
Stenotrophomonas maltophilia (Pseudomonas maltophilia)B3 metallo-beta-lactamase,Beta-lactamase type III,Metallo-beta-lactamase L1 type III,Penicillinase
ZINC IONnon-polymer65.44
5-(2-methylphenyl)-3H-1,2,4-triazole-3-thionenon-polymer189.22
SULFATE IONnon-polymer96.14
waterwater18.0518

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight57480.9
Non-Polymers*Number of molecules10
Total molecular weight1024.4
All*Total molecular weight58505.3
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.85 Å)

Cell axes105.040105.040196.990
Cell angles90.0090.00120.00
SpacegroupP 62 2 2
Resolution limits19.85 - 1.85
the highest resolution shell value1.896 - 1.850
R-factor0.1684
R-work0.16700
the highest resolution shell value0.217
R-free0.20660
the highest resolution shell value0.264
RMSD bond length0.006
RMSD bond angle0.981

Data Collection Statistics

Resolution limits19.85 - 1.85
the highest resolution shell value -
Number of reflections53574
Rmerge_l_obs0.109
the highest resolution shell value0.385
Completeness97.2
Redundancy6.8
the highest resolution shell value6.1
I/sigma(I)2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP7.757.75281

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0042597cellular_componentperiplasmic space
A0008800molecular_functionbeta-lactamase activity
A0008270molecular_functionzinc ion binding
A0017001biological_processantibiotic catabolic process
A0046677biological_processresponse to antibiotic
B0042597cellular_componentperiplasmic space
B0008800molecular_functionbeta-lactamase activity
B0008270molecular_functionzinc ion binding
B0017001biological_processantibiotic catabolic process
B0046677biological_processresponse to antibiotic
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC14binding site for residue ZN A 401
ChainResidue
AHIS105
AHIS107
AHIS181
AL3B403

AC24binding site for residue ZN A 402
ChainResidue
AASP109
AHIS110
AHIS246
AL3B403

AC315binding site for residue L3B A 403
ChainResidue
ATYR32
AHIS107
AASP109
AHIS110
AASP142
APHE145
AILE149
AHIS181
ASER206
ATYR212
AHIS246
AZN401
AZN402
AHOH542
AHOH582

AC49binding site for residue SO4 A 404
ChainResidue
AALA258
AARG259
AALA260
AGLY261
AALA262
AHOH559
AHOH563
BARG235
BLYS268

AC54binding site for residue SO4 A 405
ChainResidue
AARG158
AILE166
ATHR167
AHOH575

AC64binding site for residue SO4 A 406
ChainResidue
ATRP52
AARG91
AHOH515
AHOH553

AC74binding site for residue ZN B 401
ChainResidue
BHIS105
BHIS107
BHIS181
BL3B403

AC84binding site for residue ZN B 402
ChainResidue
BASP109
BHIS110
BHIS246
BL3B403

AC914binding site for residue L3B B 403
ChainResidue
BTYR32
BHIS105
BHIS107
BASP109
BHIS110
BPHE145
BILE149
BHIS181
BSER206
BTYR212
BHIS246
BZN401
BZN402
BHOH505

AD16binding site for residue SO4 B 404
ChainResidue
BARG158
BILE166
BTHR167
BHOH538
BHOH612
BHOH644

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
L3B_5dpx_A_403195-(2-methylphenyl)-3H-1,2,4-triazole-3-thione binding site
ChainResidueligand
ATYR32L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
ATRP38L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
AHIS105L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
AHIS107-HIS110L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
AGLY139L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
AASP142L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
AHIS144-PHE145L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
AILE149-THR150L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
AHIS181L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
ASER206L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
ASER208L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
APRO210L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
ATYR212L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
AHIS246L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione

L3B_5dpx_B_403185-(2-methylphenyl)-3H-1,2,4-triazole-3-thione binding site
ChainResidueligand
BTYR32L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
BTRP38L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
BHIS105L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
BHIS107-HIS110L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
BGLY139L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
BASP142L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
BHIS144-PHE145L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
BILE149L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
BHIS181L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
BSER206L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
BSER208L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
BPRO210L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
BTYR212L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
BHIS246L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI12Zinc 1; via tele nitrogen. {ECO:0000269|PubMed:17999929, ECO:0000269|PubMed:9811546}
ChainResidueDetails
AHIS84
AHIS160

SWS_FT_FI21Zinc 2; via tele nitrogen. {ECO:0000269|PubMed:9811546}
ChainResidueDetails
AHIS225

SWS_FT_FI31Zinc 2; via tele nitrogen. {ECO:0000269|PubMed:17999929, ECO:0000269|PubMed:9811546}
ChainResidueDetails
AHIS89

SWS_FT_FI41Zinc 2. {ECO:0000269|PubMed:17999929, ECO:0000269|PubMed:9811546}
ChainResidueDetails
AASP88

SWS_FT_FI51Zinc 1; via pros nitrogen. {ECO:0000269|PubMed:17999929, ECO:0000269|PubMed:9811546}
ChainResidueDetails
AHIS86

SWS_FT_FI61Substrate. {ECO:0000250|UniProtKB:P25910}.
ChainResidueDetails
AASP184

SWS_FT_FI72Zinc 1; via tele nitrogen. {ECO:0000269|PubMed:17999929, ECO:0000269|PubMed:9811546}
ChainResidueDetails
BHIS84
BHIS160

SWS_FT_FI81Zinc 2; via tele nitrogen. {ECO:0000269|PubMed:9811546}
ChainResidueDetails
BHIS225

SWS_FT_FI91Zinc 2; via tele nitrogen. {ECO:0000269|PubMed:17999929, ECO:0000269|PubMed:9811546}
ChainResidueDetails
BHIS89

SWS_FT_FI101Zinc 2. {ECO:0000269|PubMed:17999929, ECO:0000269|PubMed:9811546}
ChainResidueDetails
BASP88

SWS_FT_FI111Zinc 1; via pros nitrogen. {ECO:0000269|PubMed:17999929, ECO:0000269|PubMed:9811546}
ChainResidueDetails
BHIS86

SWS_FT_FI121Substrate. {ECO:0000250|UniProtKB:P25910}.
ChainResidueDetails
BASP184

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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