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Structure of thio (glycine oxidase) from bacillus subtilis

Analyse Structure of thio (glycine oxidase) from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NG4
Type: protein
Length: 728 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycine oxidase
EC: 1.5.3.-
UniProt: O31616
Ligands: FAD, PEO, PO4
Pockets: 8 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glycine oxidase (EC 1.5.3.-)	protein	364	32% helix, 28% strand	O31616

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
PEO · Hydrogen peroxide · ligand · 2 copies · chains A, B
PO4 · Phosphate ion · ion · chains A, B

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

Pockets

8 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	518	0.82	0.88	82	FAD, PEO
2	487	0.81	0.88	69	FAD, PEO
3	574	0.70	0.79	45	PO4
4	152	0.55	0.81	36	empty
5	150	0.49	0.78	17	empty

Interfaces

1 interface between chains.

A–B · 991 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

1NG4 · Structure of ThiO (glycine oxidase) from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
O31616 · AlphaFold monomer V2.0 prediction for glycine oxidase (O31616) · 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 O31616
Elsewhere: RCSB PDB 1NG4 · PDBe 1NG4 · UniProt O31616

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