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Cryo-EM structure of bluetongue virus capsid protein VP5 at low endosomal pH

Analyse Cryo-EM structure of bluetongue virus capsid protein VP5 at low endosomal pH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RTN
Type: protein
Length: 810 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer capsid protein VP5
UniProt: K7QP12
Pockets: 9 · best druggability 0.83

Structure

electron microscopy · 1 distinct chain · 51% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Outer capsid protein VP5	protein	270	51% helix, 16% strand	K7QP12

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1190	0.83	0.84	91	empty
2	626	0.67	0.77	82	empty
3	200	0.58	0.81	32	empty
4	144	0.52	0.79	25	empty
5	71	0.45	0.82	12	empty

Interfaces

3 interfaces between chains.

A–C · 1628 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 1601 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 1430 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

7RTN · Cryo-EM structure of bluetongue virus capsid protein VP5 at low endosomal pH · 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 K7QP12
Elsewhere: RCSB PDB 7RTN · PDBe 7RTN · UniProt K7QP12

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