MolNFT v1 · #114063 · protein

Crystal structure of marburg virus VP40 dimer

5B0V · Matrix protein VP40: “Crystal structure of marburg virus VP40 dimer”. X-ray diffraction, 5 pockets (best druggability 0.80). MolNFT v1 #114063 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5B0V
Type: protein
Length: 513 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Matrix protein VP40
UniProt: P35260
Pockets: 5 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Matrix protein VP40	protein	258	19% helix, 35% strand	P35260
B	Matrix protein VP40	protein	255	19% helix, 38% strand	P35260

Ligands and binding sites

EOH · Ethanol · additive · chains B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	532	0.80	0.86	47	empty
2	517	0.77	0.84	47	empty
3	87	0.42	0.79	19	empty
4	85	0.41	0.78	18	empty
5	50	0.28	0.75	15	empty

Interfaces

1 interface between chains.

A–B · 726 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 modified (engineered).

Compared structures

5B0V · Crystal Structure of Marburg virus VP40 Dimer · 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 P35260
Elsewhere: RCSB PDB 5B0V · PDBe 5B0V · UniProt P35260

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