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Cryo-EM structure of bluetongue virus capsid protein VP5 at low endosomal pH intermediate state 2

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: 7RTO
Type: protein
Length: 888 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer capsid protein VP5
UniProt: K7QP12
Pockets: 13 · best druggability 0.84

Structure

electron microscopy · 2 distinct chains · 56% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Outer capsid protein VP5	protein	270	52% helix, 16% strand	K7QP12
B	Outer capsid protein VP5	protein	348	59% helix, 12% strand	K7QP12

Pockets

13 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	1167	0.84	0.85	104	empty
2	146	0.60	0.84	22	empty
3	213	0.57	0.80	25	empty
4	289	0.55	0.75	31	empty
5	127	0.50	0.80	30	empty

Interfaces

3 interfaces between chains.

A–C · 1448 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 1424 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 1218 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7RTO · Cryo-EM structure of bluetongue virus capsid protein VP5 at low endosomal pH intermediate… · 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 7RTO · PDBe 7RTO · UniProt K7QP12

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