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Crystal structure of ebola virus VP40 hexamer

Analyse Crystal structure of ebola virus VP40 hexamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LDD
Type: protein
Length: 502 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Matrix protein VP40
UniProt: Q05128
Pockets: 8 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Matrix protein VP40	protein	226	18% helix, 37% strand	Q05128
C	Matrix protein VP40	protein	139	15% helix, 45% strand	Q05128
A	Matrix protein VP40	protein	137	15% helix, 43% strand	Q05128

Pockets

8 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	464	0.71	0.81	45	empty
2	181	0.53	0.78	26	empty
3	190	0.51	0.77	30	empty
4	150	0.50	0.78	30	empty
5	101	0.49	0.81	23	empty

Interfaces

2 interfaces between chains.

C–A · 1167 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 784 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4LDD · Crystal Structure of Ebola virus VP40 Hexamer · the same entry in another collection · chain B against B, 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 Q05128
Elsewhere: RCSB PDB 4LDD · PDBe 4LDD · UniProt Q05128

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