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Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with N-oxalylglycine (NOG)
Analyse Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NHX
- Type
- protein
- Length
- 457 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.105
- Source
- Homo sapiens
- Molecule
- 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1
- EC
- 1.14.11.-
- UniProt
- Q8N543
- Ligands
- OGA, MN, NA
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.105 · 1 distinct chain · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1 (EC 1.14.11.-) | protein | 457 | 27% helix, 31% strand | Q8N543 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · chains A
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 | 465 | 0.70 | 0.81 | 48 | empty |
| 2 | 416 | 0.66 | 0.79 | 50 | MN, OGA, GOL |
| 3 | 117 | 0.39 | 0.75 | 27 | empty |
Compared structures
- 4NHX · Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N543 · AlphaFold monomer V2.0 prediction for prolyl 3-hydroxylase OGFOD1 (Q8N543) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8N543
- Elsewhere: RCSB PDB 4NHX · PDBe 4NHX · UniProt Q8N543
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