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Structure of HIV-1 capsid protein by cryo-EM

Analyse Structure of HIV-1 capsid protein by cryo-EM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3J4F
Type: protein
Length: 1,386 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein
UniProt: Q79791
Pockets: 20 · best druggability 0.70

Structure

electron microscopy · 1 distinct chain · 59% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Capsid protein	protein	231	59% helix, 1% strand	Q79791

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.70	0.97	19	empty
2	757	0.70	0.76	73	empty
3	618	0.68	0.77	65	empty
4	484	0.67	0.78	67	empty
5	417	0.66	0.79	43	empty

Interfaces

6 interfaces between chains.

C–D · 1350 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 1316 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 1282 Å² buried · 11 hydrogen bonds · protein-protein
A–F · 1223 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1222 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3J4F · Structure of HIV-1 capsid protein by cryo-EM · 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 Q79791
Elsewhere: RCSB PDB 3J4F · PDBe 3J4F · UniProt Q79791

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