Research workbench
Crystal structure of O-ureidoserine racemase
Analyse Crystal structure of O-ureidoserine racemase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VDY
- Type
- protein
- Length
- 564 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-ureido-serine racemase
- EC
- 5.1.1.19
- UniProt
- D2Z026
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-ureido-serine racemase (EC 5.1.1.19) | protein | 285 | 16% helix, 39% strand | D2Z026 |
| B | O-ureido-serine racemase (EC 5.1.1.19) | protein | 279 | 16% helix, 40% strand | D2Z026 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.63 | 0.81 | 30 | SO4 |
| 2 | 171 | 0.60 | 0.83 | 28 | SO4 |
| 3 | 66 | 0.31 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 947 Ų buried · 16 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 D2Z026
- Elsewhere: RCSB PDB 7VDY · PDBe 7VDY · UniProt D2Z026
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