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Capsid of T5 virion

Analyse Capsid of T5 virion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OMC
Type: protein
Length: 3,883 residues
Chains: 13
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major capsid protein
UniProt: Q6QGD8
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 2 distinct chains · 16% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L	Major capsid protein	protein	299	16% helix, 20% strand	Q6QGD8
M	Major capsid protein	protein	295	17% helix, 13% strand	Q6QGD8

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	335	0.79	0.89	61	empty
2	516	0.77	0.84	62	empty
3	251	0.74	0.88	48	empty
4	82	0.74	0.96	23	empty
5	101	0.71	0.93	24	empty

Interfaces

30 interfaces between chains.

I–J · 2892 Å² buried · 46 hydrogen bonds · protein-protein
A–F · 2805 Å² buried · 45 hydrogen bonds · protein-protein
G–H · 2796 Å² buried · 39 hydrogen bonds · protein-protein
C–D · 2730 Å² buried · 39 hydrogen bonds · protein-protein
H–I · 2676 Å² buried · 38 hydrogen bonds · protein-protein

Compared structures

6OMC · capsid of T5 virion · 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 Q6QGD8
Elsewhere: RCSB PDB 6OMC · PDBe 6OMC · UniProt Q6QGD8

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