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Crystal structure of ynje

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

PDB: 3IPO
Type: protein
Length: 828 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative thiosulfate sulfurtransferase ynje
EC: 2.8.1.1
UniProt: P78067
Ligands: NA, PO4
Pockets: 10 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative thiosulfate sulfurtransferase ynje (EC 2.8.1.1)	protein	412	33% helix, 17% strand	P78067
B	Putative thiosulfate sulfurtransferase ynje (EC 2.8.1.1)	protein	416	34% helix, 17% strand	P78067

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains A, B
PG0 · 2-(2-methoxyethoxy)ethanol · additive · 2 copies · chains B
PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains B
GOL · Glycerol · additive · chains B

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

Pockets

10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	565	0.76	0.83	63	empty
2	699	0.67	0.76	65	empty
3	153	0.49	0.77	18	empty
4	145	0.48	0.77	20	empty
5	132	0.46	0.77	19	empty

Interfaces

1 interface between chains.

A–B · 738 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (oxidation).

Compared structures

3IPO · Crystal structure of YnjE · the same entry in another collection · chain A against A, TM-score 1.00
P78067 · AlphaFold monomer V2.0 prediction for thiosulfate sulfurtransferase ynje (P78067) · a predicted model of the same protein · 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 P78067
Elsewhere: RCSB PDB 3IPO · PDBe 3IPO · UniProt P78067

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