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The crystal structure of ycgj protein from bacillus subitilis

Analyse The crystal structure of ycgj protein from bacillus subitilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GLU
Type: protein
Length: 468 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ycgj
Ligands: SAM, SO4
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ycgj	protein	234	43% helix, 26% strand	—

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 11 copies · chains A, B

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

Pockets

4 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	459	0.62	0.76	48	SO4, SAM
2	321	0.58	0.77	37	SO4, SAM
3	134	0.37	0.72	26	empty
4	83	0.36	0.76	24	empty

Interfaces

1 interface between chains.

A–B · 808 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

2GLU · The crystal structure of YcgJ protein from Bacillus subitilis · 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
Elsewhere: RCSB PDB 2GLU · PDBe 2GLU

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