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Structural basis of HIV-1 capsid recognition by CPSF6

Analyse Structural basis of HIV-1 capsid recognition by CPSF6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WYM
Type: protein
Length: 2,691 residues
Chains: 23
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein P24; Isoform 2 of cleavage and polyadenylation specificity factor subunit 6
UniProt: P12497, Q16630
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 14 distinct chains · 59% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein P24	protein	214	57% helix, 3% strand	P12497
B	Capsid protein P24	protein	213	62% helix, 3% strand	P12497
C	Capsid protein P24	protein	212	61% helix, 3% strand	P12497
D	Capsid protein P24	protein	204	58% helix, 3% strand	P12497
E	Capsid protein P24	protein	215	60% helix, 3% strand	P12497
F	Capsid protein P24	protein	220	60% helix, 3% strand	P12497
G, H	Capsid protein P24	protein	211	58% helix, 3% strand	P12497
I	Capsid protein P24	protein	212	58% helix, 3% strand	P12497
J	Capsid protein P24	protein	213	61% helix, 3% strand	P12497
K	Capsid protein P24	protein	210	60% helix, 3% strand	P12497
L	Capsid protein P24	protein	208	62% helix, 3% strand	P12497
M, O, Q, T, U, V, W	Isoform 2 of cleavage and polyadenylation specificity factor subunit 6	protein	13	0% helix, 0% strand	Q16630
N, P, R	Isoform 2 of cleavage and polyadenylation specificity factor subunit 6	protein	14	0% helix, 0% strand	Q16630
S	Isoform 2 of cleavage and polyadenylation specificity factor subunit 6	protein	15	0% helix, 0% strand	Q16630

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1173	0.80	0.81	135	empty
2	780	0.77	0.81	99	empty
3	785	0.77	0.81	95	empty
4	555	0.75	0.82	78	empty
5	81	0.74	0.97	19	empty

Interfaces

63 interfaces between chains.

J–K · 1374 Å² buried · 12 hydrogen bonds · protein-protein
G–L · 1358 Å² buried · 14 hydrogen bonds · protein-protein
A–F · 1333 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1286 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 1286 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

Q16630 · AlphaFold monomer V2.0 prediction for cleavage and polyadenylation specificity factor… · a predicted model of the same protein · chain Q against A, TM-score 0.35

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
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Elsewhere: RCSB PDB 4WYM · PDBe 4WYM · UniProt P12497 · UniProt Q16630

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