Research workbench
Crystal structure of the human 2-oxoglutarate oxygenase LOC390245
Analyse Crystal structure of the human 2-oxoglutarate oxygenase LOC390245 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W2I
- Type
- protein
- Length
- 925 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-oxoglutarate oxygenase
- UniProt
- B2RXH2
- Ligands
- PD2, NI
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-oxoglutarate oxygenase | protein | 305 | 28% helix, 29% strand | B2RXH2 |
| B | 2-oxoglutarate oxygenase | protein | 306 | 29% helix, 28% strand | B2RXH2 |
| C | 2-oxoglutarate oxygenase | protein | 314 | 30% helix, 28% strand | B2RXH2 |
Ligands and binding sites
- PD2 · Pyridine-2,4-dicarboxylic acid · ligand · 3 copies · chains A, B, C
- NI · Nickel (II) ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 5 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.68 | 0.85 | 32 | NI, PD2 |
| 2 | 224 | 0.67 | 0.84 | 34 | NI, PD2 |
| 3 | 219 | 0.66 | 0.84 | 33 | NI, PD2 |
| 4 | 145 | 0.43 | 0.75 | 24 | empty |
| 5 | 112 | 0.39 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 496 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 250 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 96 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2W2I · Crystal structure of the human 2-oxoglutarate oxygenase LOC390245 · the same entry in another collection · chain A against A, TM-score 1.00
- B2RXH2 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 4E (B2RXH2) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 B2RXH2
- Elsewhere: RCSB PDB 2W2I · PDBe 2W2I · UniProt B2RXH2
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