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HIV-1 ca hexamer with NUP153 peptide - P1 crystal form

Analyse HIV-1 ca hexamer with NUP153 peptide - P1 crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TSX
Type: protein
Length: 2,633 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 ca protein; Nuclear pore complex protein NUP153
UniProt: P12493, P49790
Ligands: FLU
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 11 distinct chains · 60% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, G	HIV-1 ca protein	protein	219	59% helix, 3% strand	P12493
C	HIV-1 ca protein	protein	215	62% helix, 3% strand	P12493
D, E, F	HIV-1 ca protein	protein	214	63% helix, 3% strand	P12493
H	HIV-1 ca protein	protein	216	60% helix, 3% strand	P12493
I	HIV-1 ca protein	protein	207	60% helix, 3% strand	P12493
J	HIV-1 ca protein	protein	212	59% helix, 3% strand	P12493
K	HIV-1 ca protein	protein	213	63% helix, 3% strand	P12493
L	HIV-1 ca protein	protein	211	64% helix, 3% strand	P12493
M, N	Nuclear pore complex protein NUP153	protein	11	0% helix, 0% strand	P49790
O	Nuclear pore complex protein NUP153	protein	11	0% helix, 0% strand	P49790
P, R, T	Nuclear pore complex protein NUP153	protein	9	0% helix, 0% strand	P49790

Ligands and binding sites

FLU · 2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-benzoic acid · ligand · 4 copies · chains A, B, G, H

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	765	0.77	0.81	97	empty
2	712	0.76	0.81	102	empty
3	684	0.76	0.81	100	empty
4	559	0.75	0.82	87	empty
5	450	0.72	0.82	65	empty

Interfaces

40 interfaces between chains.

G–L · 1423 Å² buried · 11 hydrogen bonds · protein-protein
A–E · 1408 Å² buried · 16 hydrogen bonds · protein-protein
B–F · 1405 Å² buried · 16 hydrogen bonds · protein-protein
H–K · 1403 Å² buried · 12 hydrogen bonds · protein-protein
D–I · 1311 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

5TSX · HIV-1 CA hexamer with NUP153 peptide - P1 crystal form · the same entry in another collection · chain T against T, 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 P49790
Elsewhere: RCSB PDB 5TSX · PDBe 5TSX · UniProt P12493 · UniProt P49790

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