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Structure paper

TitleLigand screen against Enterococcus faecium VatD
Journal, issue, pagesTo be published
Publish dateJan 25, 2025 (structure data deposition date)
AuthorsAsthana, P. / Fraser, J.S.
External linksSearch PubMed
MethodsX-ray diffraction
Resolution1.73 - 2.38 Å
Structure data

PDB-7hzv:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000000438614
Method: X-RAY DIFFRACTION / Resolution: 2.28 Å

PDB-7hzw:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000000039994
Method: X-RAY DIFFRACTION / Resolution: 2.06 Å

PDB-7hzx:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000000164888
Method: X-RAY DIFFRACTION / Resolution: 2.36 Å

PDB-7hzy:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000002977810
Method: X-RAY DIFFRACTION / Resolution: 2.03 Å

PDB-7hzz:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000000001712
Method: X-RAY DIFFRACTION / Resolution: 2.09 Å

PDB-7i00:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000084843283
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-7i01:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000000388593
Method: X-RAY DIFFRACTION / Resolution: 2.16 Å

PDB-7i02:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000000873830
Method: X-RAY DIFFRACTION / Resolution: 2.38 Å

PDB-7i03:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000027858187
Method: X-RAY DIFFRACTION / Resolution: 2.16 Å

PDB-7i04:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000002561227
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7i05:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000016889973
Method: X-RAY DIFFRACTION / Resolution: 1.97 Å

PDB-7i06:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000001389101
Method: X-RAY DIFFRACTION / Resolution: 1.81 Å

PDB-7i07:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000001683100
Method: X-RAY DIFFRACTION / Resolution: 1.91 Å

PDB-7i08:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000004976927
Method: X-RAY DIFFRACTION / Resolution: 2.28 Å

PDB-7i09:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000020269204
Method: X-RAY DIFFRACTION / Resolution: 2.04 Å

PDB-7i0a:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000004774482
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-7i0b:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000042783023
Method: X-RAY DIFFRACTION / Resolution: 2.11 Å

PDB-7i0c:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000000388332
Method: X-RAY DIFFRACTION / Resolution: 2.11 Å

PDB-7i0d:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000019074717
Method: X-RAY DIFFRACTION / Resolution: 2.11 Å

PDB-7i0e:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000000164607
Method: X-RAY DIFFRACTION / Resolution: 1.96 Å

PDB-7i0f:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000000056439
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7i0g:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000000158650
Method: X-RAY DIFFRACTION / Resolution: 2.05 Å

PDB-7i0h:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000006490906
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-7i0i:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000001698894
Method: X-RAY DIFFRACTION / Resolution: 1.88 Å

PDB-7i0j:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000000090873
Method: X-RAY DIFFRACTION / Resolution: 1.99 Å

PDB-7i0k:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000001722141
Method: X-RAY DIFFRACTION / Resolution: 1.99 Å

PDB-7i0l:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000016697555
Method: X-RAY DIFFRACTION / Resolution: 1.97 Å

PDB-7i0m:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with Z1302549938
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-7i0n:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with Z2440817672
Method: X-RAY DIFFRACTION / Resolution: 2.26 Å

PDB-7i0o:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with Z747549372
Method: X-RAY DIFFRACTION / Resolution: 1.98 Å

PDB-7i0p:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with Z287010572
Method: X-RAY DIFFRACTION / Resolution: 2.27 Å

PDB-7i0q:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with PV-006358264279
Method: X-RAY DIFFRACTION / Resolution: 1.93 Å

PDB-7i0r:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with Z1263798799
Method: X-RAY DIFFRACTION / Resolution: 1.73 Å

PDB-7i0s:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with Z2046612904
Method: X-RAY DIFFRACTION / Resolution: 1.88 Å

PDB-7i0t:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with Z4090027317
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-7i0u:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with Z798857536
Method: X-RAY DIFFRACTION / Resolution: 2.37 Å

PDB-7i0v:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with Z1441867474
Method: X-RAY DIFFRACTION / Resolution: 2.02 Å

PDB-7i0w:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with Z5440841580
Method: X-RAY DIFFRACTION / Resolution: 2.09 Å

PDB-7i0x:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with Z2301759489
Method: X-RAY DIFFRACTION / Resolution: 1.88 Å

PDB-7i0y:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with Z790365490
Method: X-RAY DIFFRACTION / Resolution: 1.84 Å

PDB-7i0z:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with Z1500734581
Method: X-RAY DIFFRACTION / Resolution: 1.87 Å

PDB-7i10:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with Z295930154
Method: X-RAY DIFFRACTION / Resolution: 1.84 Å

PDB-7i11:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with Z1152041263
Method: X-RAY DIFFRACTION / Resolution: 1.84 Å

PDB-7i12:
PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with Z3562614682
Method: X-RAY DIFFRACTION / Resolution: 1.94 Å

Chemicals

ChemComp-W6G:
N-(1,3,4-thiadiazol-2-yl)benzenesulfonamide

ChemComp-HOH:
WATER

ChemComp-W6V:
N-(1,3-thiazol-2-yl)benzamide

ChemComp-YTP:
1-(4-hydroxy-3-methylphenyl)ethanone

ChemComp-2AK:
7-bromo-5-methyl-1H-indole-2,3-dione

ChemComp-MPB:
4-HYDROXY-BENZOIC ACID METHYL ESTER

ChemComp-CLW:
CHLORZOXAZONE

ChemComp-DMD:
5,6-DIMETHYLBENZIMIDAZOLE

ChemComp-NMI:
3-(1-methyl-1H-indol-3-yl)propanoic acid

ChemComp-EVD:
1-benzofuran-2-sulfonamide

ChemComp-47S:
3-(dimethylamino)benzohydrazide

ChemComp-AX7:
1H-benzimidazol-2-amine

ChemComp-7MU:
4-chloranyl-~{N}-methyl-pyridine-2-carboxamide

ChemComp-W6A:
4-chloro-1H-indole-2-carboxylic acid

ChemComp-04R:
[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]acetic acid

PDB-1buq:
SOLUTION STRUCTURE OF DELTA-5-3-KETOSTEROID ISOMERASE COMPLEXED WITH THE STEROID 19-NORTESTOSTERONE-HEMISUCCINATE

PDB-1h0m:
Three-dimensional structure of the quorum sensing protein TraR bound to its autoinducer and to its target DNA

ChemComp-80Q:
2-piperidin-4-yloxy-5-(trifluoromethyl)pyridine

ChemComp-4FA:
4-FLUOROPHENETHYL ALCOHOL

ChemComp-2AQ:
QUINOLIN-2-AMINE

ChemComp-8P7:
2-methyl-1~{H}-benzimidazole

ChemComp-WL3:
2-(4-fluorophenyl)carbonylbenzoic acid

ChemComp-XIY:
2-HYDROXYMETHYL-BENZOIMIDAZOLE

ChemComp-EVE:
1H-benzimidazole-2-sulfonamide

ChemComp-PF0:
3-hydroxy-2-methylbenzoic acid

ChemComp-6OT:
3,5-dichlorobenzene-1-sulfonamide

ChemComp-2HQ:
5-chloro-1H-indole-2,3-dione

ChemComp-LVF:
2-(5-chloranyl-1H-indol-3-yl)ethanenitrile

PDB-1bvd:
STRUCTURE OF A BILIVERDIN APOMYOGLOBIN COMPLEX (FORM B) AT 98 K

PDB-1bu2:
X-RAY STRUCTURE OF A VIRAL CYCLIN FROM HERPESVIRUS SAIMIRI

PDB-1bve:
HIV-1 PROTEASE-DMP323 COMPLEX IN SOLUTION, NMR, 28 STRUCTURES

PDB-1bvf:
Unknown entry

PDB-1bvg:
HIV-1 PROTEASE-DMP323 COMPLEX IN SOLUTION, NMR MINIMIZED AVERAGE STRUCTURE

PDB-1bus:
SOLUTION CONFORMATION OF PROTEINASE INHIBITOR IIA FROM BULL SEMINAL PLASMA BY 1H NUCLEAR MAGNETIC RESONANCE AND DISTANCE GEOMETRY

PDB-1but:
NMR STRUCTURE OF THE DNA DECAMER D(CATGGCCATG)2, 10 STRUCTURES

PDB-1buu:
ONE HO3+ FORM OF RAT MANNOSE-BINDING PROTEIN A

PDB-1buv:
CRYSTAL STRUCTURE OF THE MT1-MMP-TIMP-2 COMPLEX

PDB-1bvh:
SOLUTION STRUCTURE OF A LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE

PDB-1bux:
3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE

PDB-1buw:
CRYSTAL STRUCTURE OF S-NITROSO-NITROSYL HUMAN HEMOGLOBIN A

PDB-1buy:
HUMAN ERYTHROPOIETIN, NMR MINIMIZED AVERAGE STRUCTURE

PDB-1buz:
SOLUTION STRUCTURE OF SPOIIAA, A PHOSPHORYLATABLE COMPONENT OF THE SYSTEM THAT REGULATES TRANSCRIPTION FACTOR SIGMA-F OF BACILLUS SUBTILIS NMR, MINIMIZED AVERAGE STRUCTURE

PDB-1bu0:
Unknown entry

PDB-1bu1:
SRC FAMILY KINASE HCK SH3 DOMAIN

Source
  • enterococcus faecium (bacteria)
KeywordsTRANSFERASE / VatD / antibiotic resistance / streptogramin / fragment-based drug discovery

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