Research workbench
Crystal structure of glycine oxidase from geobacillus kaustophilus
Analyse Crystal structure of glycine oxidase from geobacillus kaustophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YSH
- Type
- protein
- Length
- 738 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine oxidase
- EC
- 1.4.3.19
- UniProt
- Q5L2C2
- Ligands
- FAD, GLY, SO4, CL
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine oxidase (EC 1.4.3.19) | protein | 370 | 32% helix, 27% strand | Q5L2C2 |
| B | Glycine oxidase (EC 1.4.3.19) | protein | 368 | 33% helix, 28% strand | Q5L2C2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- GLY · Glycine · ligand · 2 copies · chains B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · chains B
- IPA · Isopropyl alcohol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.81 | 0.91 | 61 | GLY, FAD |
| 2 | 502 | 0.79 | 0.86 | 69 | FAD |
| 3 | 800 | 0.72 | 0.78 | 90 | empty |
| 4 | 162 | 0.46 | 0.76 | 36 | GLY |
| 5 | 55 | 0.45 | 0.84 | 14 | IPA |
Interfaces
1 interface between chains.
- A–B · 483 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 Q5L2C2
- Elsewhere: RCSB PDB 4YSH · PDBe 4YSH · UniProt Q5L2C2
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