Research workbench

X-ray structure of hexameric HIV-1 ca

Analyse X-ray structure of hexameric HIV-1 ca in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GV2
Type: protein
Length: 1,314 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein P24,CARBON dioxide-concentrating mechanism protein ccmk homolog 4
UniProt: P12493, P73407
Pockets: 20 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 59% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Capsid protein P24,CARBON dioxide-concentrating mechanism protein ccmk homolog 4	protein	219	59% helix, 3% strand	P12493, P73407

Pockets

20 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	595	0.57	0.72	110	empty
2	319	0.51	0.74	43	empty
3	288	0.48	0.73	42	empty
4	264	0.46	0.73	41	empty
5	262	0.45	0.73	48	empty

Interfaces

6 interfaces between chains.

C–D · 128 Å² buried · 0 hydrogen bonds · protein-protein
A–F · 126 Å² buried · 0 hydrogen bonds · protein-protein
E–F · 119 Å² buried · 0 hydrogen bonds · protein-protein
D–E · 116 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 110 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3GV2 · X-ray Structure of Hexameric HIV-1 CA · the same entry in another collection · chain F against F, TM-score 1.00
P73407 · AlphaFold monomer V2.0 prediction for carboxysome shell protein CCMK4 (P73407) · a predicted model of the same protein · chain E against A, TM-score 0.19

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 P12493
Every structure of UniProt P73407
Elsewhere: RCSB PDB 3GV2 · PDBe 3GV2 · UniProt P12493 · UniProt P73407

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