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Ebola virus VP35 bound to small molecule

Analyse Ebola virus VP35 bound to small molecule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4IBG
Type: protein
Length: 246 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polymerase cofactor VP35
UniProt: Q05127
Ligands: 1D6, SO4, PO4
Pockets: 1 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Polymerase cofactor VP35	protein	123	54% helix, 13% strand	Q05127

Ligands and binding sites

1D6 · {4-[(2S)-2-(7-chloro-1,3-benzodioxol-5-yl)-4-hydroxy-3-(3-methylbenzoyl)-5-oxo-2,5-dihydro-1H-pyrrol-1-yl]phenyl}acetic acid · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B
PO4 · Phosphate ion · ion · chains A, B
GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	890	0.71	0.76	71	1D6, GOL, PO4

Interfaces

1 interface between chains.

A–B · 249 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4IBG · Ebola virus VP35 bound to small molecule · 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 Q05127
Elsewhere: RCSB PDB 4IBG · PDBe 4IBG · UniProt Q05127

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