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Hexamer of helical HIV capsid by rastr method

Analyse Hexamer of helical HIV capsid by rastr method in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VWS
Type: protein
Length: 1,320 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV capsid protein
UniProt: B6DRA0
Pockets: 12 · best druggability 0.82

Structure

electron microscopy · 1 distinct chain · 44% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, M, N	HIV capsid protein	protein	220	44% helix, 3% strand	B6DRA0

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1016	0.82	0.83	163	empty
2	741	0.79	0.83	110	empty
3	310	0.68	0.83	58	empty
4	684	0.65	0.75	77	empty
5	473	0.60	0.75	54	empty

Interfaces

6 interfaces between chains.

D–N · 339 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 335 Å² buried · 0 hydrogen bonds · protein-protein
A–M · 260 Å² buried · 0 hydrogen bonds · protein-protein
M–N · 238 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 235 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6VWS · Hexamer of Helical HIV capsid by RASTR method · 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 B6DRA0
Elsewhere: RCSB PDB 6VWS · PDBe 6VWS · UniProt B6DRA0

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