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YCJX-GDPCP

Analyse YCJX-GDPCP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NZ5
Type: protein
Length: 912 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ycjx stress protein
UniProt: Q8EG04
Ligands: GCP, GDP
Pockets: 9 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ycjx stress protein	protein	458	39% helix, 17% strand	Q8EG04
B	Ycjx stress protein	protein	454	39% helix, 18% strand	Q8EG04

Ligands and binding sites

GCP · Phosphomethylphosphonic acid guanylate ester · ligand · chains A
GDP · Guanosine-5'-diphosphate · ligand · chains B

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1032	0.74	0.77	93	empty
2	471	0.65	0.77	72	empty
3	343	0.65	0.80	49	GDP
4	285	0.64	0.81	41	GCP
5	126	0.50	0.80	23	empty

Interfaces

1 interface between chains.

A–B · 1011 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6NZ5 · YcjX-GDPCP · 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 6NZ5 · PDBe 6NZ5 · UniProt Q8EG04

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