MolNFT v1 · #158605 · protein

Ycjx-GDP (type II)

6NZ6 · Ycjx stress protein: “Ycjx-GDP (type II)”. X-ray diffraction, 1 ligand (GDP), 11 pockets (best druggability 0.70). MolNFT v1 #158605 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6NZ6
Type: protein
Length: 909 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 0.70

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ycjx stress protein	protein	458	40% helix, 17% strand	Q8EG04
B	Ycjx stress protein	protein	451	41% 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	509	0.70	0.80	41	empty
2	333	0.69	0.82	51	GDP
3	342	0.68	0.81	56	GDP
4	234	0.60	0.80	43	empty
5	242	0.54	0.77	43	empty

Interfaces

1 interface between chains.

A–B · 1193 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6NZ6 · YcjX-GDP (type II) · 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 6NZ6 · PDBe 6NZ6 · UniProt Q8EG04

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