Research workbench
Crystal structure of OFD2 in complex with 2OG from schizosaccharomyces pombe
Analyse Crystal structure of OFD2 in complex with 2OG from schizosaccharomyces pombe in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YL6
- Type
- protein
- Length
- 184 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein P8A3.02C
- UniProt
- Q9UT12
- Ligands
- AKG, FE
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein P8A3.02C | protein | 184 | 22% helix, 38% strand | Q9UT12 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- FE · Fe (III) ion · metal · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.55 | 0.81 | 26 | FE, AKG, ACT |
| 2 | 69 | 0.29 | 0.73 | 16 | empty |
Compared structures
- 5YL6 · Crystal structure of Ofd2 in complex with 2OG from Schizosaccharomyces pombe · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UT12 · AlphaFold monomer V2.0 prediction for uncharacterized protein P8A3.02C (Q9UT12) · 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 Q9UT12
- Elsewhere: RCSB PDB 5YL6 · PDBe 5YL6 · UniProt Q9UT12
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