MolNFT v1 · #107119 · protein

Hexameric HIV-1 ca in complex with NUP153 peptide, P212121 crystal form

4U0D · Gag polyprotein: “Hexameric HIV-1 ca in complex with NUP153 peptide, P212121 crystal form”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.69). MolNFT v1 #107119 on GenesisL1: 3D structure, binding sites and…

PDB: 4U0D
Type: protein
Length: 2,512 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gag polyprotein; Nuclear pore complex protein NUP153
UniProt: P12493, P49790
Ligands: CL
Pockets: 20 · best druggability 0.69

Structure

x-ray diffraction · 11 distinct chains · 61% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gag polyprotein	protein	216	61% helix, 2% strand	P12493
B	Gag polyprotein	protein	207	65% helix, 2% strand	P12493
C	Gag polyprotein	protein	211	62% helix, 2% strand	P12493
D	Gag polyprotein	protein	210	60% helix, 2% strand	P12493
E	Gag polyprotein	protein	192	63% helix, 2% strand	P12493
F	Gag polyprotein	protein	211	62% helix, 2% strand	P12493
G	Gag polyprotein	protein	212	62% helix, 2% strand	P12493
H, J, K	Gag polyprotein	protein	204	58% helix, 2% strand	P12493
I	Gag polyprotein	protein	196	61% helix, 2% strand	P12493
L	Gag polyprotein	protein	191	63% helix, 2% strand	P12493
M, N, O, P, Q, R	Nuclear pore complex protein NUP153	protein	9	0% helix, 0% strand	P49790

Ligands and binding sites

CL · Chloride ion · ion · chains E, F

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	750	0.69	0.76	65	empty
2	664	0.68	0.77	62	empty
3	649	0.68	0.76	56	empty
4	488	0.67	0.78	63	empty
5	481	0.65	0.77	63	empty

Interfaces

35 interfaces between chains.

D–E · 1232 Å² buried · 10 hydrogen bonds · protein-protein
A–F · 1210 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 1208 Å² buried · 10 hydrogen bonds · protein-protein
J–K · 1200 Å² buried · 10 hydrogen bonds · protein-protein
G–L · 1195 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

4U0D · Hexameric HIV-1 CA in complex with Nup153 peptide, P212121 crystal form · the same entry in another collection · chain R against R, 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 4U0D · PDBe 4U0D · UniProt P12493 · UniProt P49790

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