MolNFT v1 · #88225 · protein

HIV-1 capsid C-terminal domain mutant (Y169L)

4COC · Capsid protein P24: “HIV-1 capsid C-terminal domain mutant (Y169L)”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.57). MolNFT v1 #88225 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4COC
Type: protein
Length: 227 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein P24
UniProt: P12497
Ligands: SO4
Pockets: 2 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 63% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein P24	protein	75	65% helix, 0% strand	P12497
B	Capsid protein P24	protein	79	62% helix, 0% strand	P12497
C	Capsid protein P24	protein	73	62% helix, 0% strand	P12497

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	117	0.57	0.84	15	empty
2	142	0.43	0.76	23	empty

Interfaces

2 interfaces between chains.

A–B · 716 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 299 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4COC · HIV-1 capsid C-terminal domain mutant (Y169L) · 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 P12497
Elsewhere: RCSB PDB 4COC · PDBe 4COC · UniProt P12497

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