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Structure of glycine oxidase with bound inhibitor glycolate

Analyse Structure of glycine oxidase with bound inhibitor glycolate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RYI
Type: protein
Length: 1,456 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycine oxidase
EC: 1.4.3.19
UniProt: O31616
Ligands: FAD, GOA
Pockets: 14 · best druggability 0.89

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Glycine oxidase (EC 1.4.3.19)	protein	364	32% helix, 28% strand	O31616

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
GOA · Glycolic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

14 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	1142	0.89	0.91	162	FAD, GOA
2	486	0.82	0.89	72	FAD, GOA
3	498	0.81	0.88	74	FAD, GOA
4	157	0.59	0.83	22	empty
5	144	0.50	0.79	16	empty

Interfaces

4 interfaces between chains.

C–D · 886 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 530 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 515 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 67 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1RYI · Structure of glycine oxidase with bound inhibitor glycolate · 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 1RYI · PDBe 1RYI · UniProt O31616

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