MolNFT v1 · #107117 · protein

Hexamer HIV-1 ca in complex with CPSF6 peptide, P212121 crystal form

4U0B · Capsid protein P24: “Hexamer HIV-1 ca in complex with CPSF6 peptide, P212121 crystal form”. X-ray diffraction, 20 pockets (best druggability 0.76). MolNFT v1 #107117 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4U0B
Type: protein
Length: 2,596 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein P24; Cleavage and polyadenylation specificity factor subunit 6
UniProt: P12493, Q16630
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 11 distinct chains · 62% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein P24	protein	208	64% helix, 2% strand	P12493
B	Capsid protein P24	protein	201	61% helix, 2% strand	P12493
C, E, G, J	Capsid protein P24	protein	198	63% helix, 2% strand	P12493
D	Capsid protein P24	protein	203	61% helix, 2% strand	P12493
F	Capsid protein P24	protein	207	65% helix, 2% strand	P12493
H	Capsid protein P24	protein	202	64% helix, 2% strand	P12493
I	Capsid protein P24	protein	211	60% helix, 2% strand	P12493
K	Capsid protein P24	protein	197	64% helix, 2% strand	P12493
L	Capsid protein P24	protein	208	64% helix, 2% strand	P12493
M, O, P, Q, R, S, T, U, V, W, X	Cleavage and polyadenylation specificity factor subunit 6	protein	14	0% helix, 0% strand	Q16630
N	Cleavage and polyadenylation specificity factor subunit 6	protein	13	0% helix, 0% strand	Q16630

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	441	0.76	0.85	35	empty
2	815	0.75	0.79	80	empty
3	730	0.75	0.80	69	empty
4	767	0.74	0.79	70	empty
5	512	0.73	0.82	73	empty

Interfaces

48 interfaces between chains.

H–I · 1295 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1292 Å² buried · 12 hydrogen bonds · protein-protein
G–L · 1283 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1280 Å² buried · 9 hydrogen bonds · protein-protein
I–J · 1266 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

4U0B · Hexamer HIV-1 CA in complex with CPSF6 peptide, P212121 crystal form · the same entry in another collection · chain K against K, 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
Every structure of UniProt Q16630
Elsewhere: RCSB PDB 4U0B · PDBe 4U0B · UniProt P12493 · UniProt Q16630

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