MolNFT v1 · #52541 · protein

Structure of the evf virulence factor

2W3Y: “Structure of the evf virulence factor”. X-ray diffraction, 1 ligand (PLM), 4 pockets (best druggability 0.82). MolNFT v1 #52541 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2W3Y
Type: protein
Length: 528 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Virulence factor
UniProt: Q8GCR2
Ligands: PLM
Pockets: 4 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Virulence factor	protein	267	43% helix, 31% strand	Q8GCR2
B	Virulence factor	protein	261	45% helix, 31% strand	Q8GCR2

Ligands and binding sites

PLM · Palmitic acid · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	167	0.82	0.97	26	PLM
2	156	0.81	0.97	26	PLM
3	833	0.75	0.80	62	empty
4	79	0.45	0.81	18	empty

Interfaces

1 interface between chains.

A–B · 524 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 lipid (palmitoylation).

Compared structures

2W3Y · Structure of the Evf virulence factor · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q8GCR2
Elsewhere: RCSB PDB 2W3Y · PDBe 2W3Y · UniProt Q8GCR2

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