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Ycjx-GDP (type I)

Analyse Ycjx-GDP (type I) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NZ4
Type: protein
Length: 918 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ycjx stress protein
UniProt: Q8EG04
Ligands: GDP
Pockets: 11 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ycjx stress protein	protein	467	41% helix, 17% strand	Q8EG04
B	Ycjx stress protein	protein	451	42% helix, 18% strand	Q8EG04

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	598	0.73	0.80	61	empty
2	367	0.65	0.80	40	empty
3	267	0.65	0.82	45	GDP
4	299	0.65	0.81	46	GDP
5	257	0.55	0.77	44	empty

Interfaces

1 interface between chains.

A–B · 1151 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6NZ4 · YcjX-GDP (type I) · 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 Q8EG04
Elsewhere: RCSB PDB 6NZ4 · PDBe 6NZ4 · UniProt Q8EG04

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