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HIV-1 ca hexamer in complex with IP6, orthorhombic crystal form

Analyse HIV-1 ca hexamer in complex with IP6, orthorhombic crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BHT
Type: protein
Length: 2,551 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein P24
UniProt: P12493
Ligands: IHP
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 11 distinct chains · 61% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein P24	protein	219	59% helix, 3% strand	P12493
B	Capsid protein P24	protein	209	59% helix, 3% strand	P12493
C	Capsid protein P24	protein	219	60% helix, 3% strand	P12493
D	Capsid protein P24	protein	209	61% helix, 3% strand	P12493
E	Capsid protein P24	protein	211	61% helix, 3% strand	P12493
F, H	Capsid protein P24	protein	221	58% helix, 3% strand	P12493
G	Capsid protein P24	protein	216	60% helix, 3% strand	P12493
I	Capsid protein P24	protein	216	60% helix, 3% strand	P12493
J	Capsid protein P24	protein	207	63% helix, 3% strand	P12493
K	Capsid protein P24	protein	201	63% helix, 3% strand	P12493
L	Capsid protein P24	protein	202	63% helix, 3% strand	P12493

Ligands and binding sites

IHP · Inositol hexakisphosphate · ligand · 4 copies · chains A, B, C, D, F, E, G, H, I, J, K, L

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

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	732	0.73	0.79	89	empty
2	806	0.73	0.78	98	empty
3	518	0.72	0.81	67	empty
4	630	0.72	0.79	81	empty
5	474	0.71	0.81	67	empty

Interfaces

32 interfaces between chains.

E–F · 1469 Å² buried · 13 hydrogen bonds · protein-protein
A–F · 1433 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 1325 Å² buried · 11 hydrogen bonds · protein-protein
H–I · 1320 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1299 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

6BHT · HIV-1 CA hexamer in complex with IP6, orthorhombic crystal form · 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 P12493
Elsewhere: RCSB PDB 6BHT · PDBe 6BHT · UniProt P12493

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