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The atomic structure of varicella-zoster virus A-capsid

Analyse The atomic structure of varicella-zoster virus A-capsid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LGL
Type: protein
Length: 26,719 residues
Chains: 46
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 4.4
Source: Human herpesvirus 3
Molecule: Major capsid protein; Small capsomere-interacting protein; Triplex capsid protein 1…
UniProt: Q6QCL5, Q6QCN2, Q6QCN5, Q6QCL4
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · resolution 4.4 · 23 distinct chains · 26% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, Q, T, C, F	Major capsid protein	protein	1354	26% helix, 18% strand	Q6QCL5
D, V, W, X, Y, Z, a, c, d, I, J, K, L	Small capsomere-interacting protein	protein	100	35% helix, 0% strand	Q6QCN2
M, N, R	Major capsid protein	protein	1353	27% helix, 17% strand	Q6QCL5
O, P, S, B	Major capsid protein	protein	1355	27% helix, 17% strand	Q6QCL5
b, H	Small capsomere-interacting protein	protein	99	33% helix, 2% strand	Q6QCN2
U	Major capsid protein	protein	1331	23% helix, 13% strand	Q6QCL5
E	Major capsid protein	protein	1353	28% helix, 16% strand	Q6QCL5
G	Major capsid protein	protein	1295	22% helix, 13% strand	Q6QCL5
e	Triplex capsid protein 1	protein	275	23% helix, 28% strand	Q6QCN5
j	Triplex capsid protein 2	protein	241	27% helix, 20% strand	Q6QCL4
o	Triplex capsid protein 2	protein	258	23% helix, 21% strand	Q6QCL4
f	Triplex capsid protein 1	protein	351	28% helix, 23% strand	Q6QCN5
k	Triplex capsid protein 2	protein	289	28% helix, 18% strand	Q6QCL4
p	Triplex capsid protein 2	protein	301	31% helix, 20% strand	Q6QCL4
g	Triplex capsid protein 1	protein	307	21% helix, 27% strand	Q6QCN5
l	Triplex capsid protein 2	protein	262	27% helix, 21% strand	Q6QCL4
q	Triplex capsid protein 2	protein	254	28% helix, 21% strand	Q6QCL4
h	Triplex capsid protein 1	protein	340	28% helix, 25% strand	Q6QCN5
m, n	Triplex capsid protein 2	protein	276	25% helix, 21% strand	Q6QCL4
r	Triplex capsid protein 2	protein	301	34% helix, 18% strand	Q6QCL4
i	Triplex capsid protein 1	protein	353	27% helix, 26% strand	Q6QCN5
s	Triplex capsid protein 2	protein	302	34% helix, 20% strand	Q6QCL4
z	Major capsid protein	protein	607	25% helix, 16% strand	Q6QCL5

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	977	0.90	0.92	128	empty
2	877	0.89	0.92	111	empty
3	1877	0.88	0.90	175	empty
4	1146	0.88	0.90	98	empty
5	1449	0.88	0.90	142	empty

Interfaces

131 interfaces between chains.

E–F · 6118 Å² buried · 80 hydrogen bonds · protein-protein
F–G · 5887 Å² buried · 65 hydrogen bonds · protein-protein
U–B · 5835 Å² buried · 63 hydrogen bonds · protein-protein
A–M · 5796 Å² buried · 58 hydrogen bonds · protein-protein
C–E · 5772 Å² buried · 57 hydrogen bonds · protein-protein

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 Q6QCL5
Every structure of UniProt Q6QCN2
Every structure of UniProt Q6QCN5
Every structure of UniProt Q6QCL4
Elsewhere: RCSB PDB 6LGL · PDBe 6LGL · UniProt Q6QCL5 · UniProt Q6QCN2 · UniProt Q6QCN5 · UniProt Q6QCL4

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