Research workbench
Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with pyridine-2,4- dicarboxylic acid (2,4-pdca)
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
- 4NHY
- Type
- protein
- Length
- 1,840 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-oxoglutarate and iron-dependent oxygenase domain- containing protein 1
- EC
- 1.14.11.-
- UniProt
- Q8N543
- Ligands
- PD2, MN
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | 2-oxoglutarate and iron-dependent oxygenase domain- containing protein 1 (EC 1.14.11.-) | protein | 461 | 28% helix, 31% strand | Q8N543 |
| C | 2-oxoglutarate and iron-dependent oxygenase domain- containing protein 1 (EC 1.14.11.-) | protein | 457 | 26% helix, 32% strand | Q8N543 |
Ligands and binding sites
- PD2 · Pyridine-2,4-dicarboxylic acid · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.83 | 0.84 | 93 | empty |
| 2 | 1109 | 0.82 | 0.84 | 108 | empty |
| 3 | 1087 | 0.81 | 0.82 | 117 | MN, GOL, PD2 |
| 4 | 448 | 0.79 | 0.88 | 45 | empty |
| 5 | 951 | 0.78 | 0.80 | 85 | PD2 |
Interfaces
6 interfaces between chains.
- A–B · 1041 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 559 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 395 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 320 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 151 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4NHY · 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 0.99
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 Q8N543
- Elsewhere: RCSB PDB 4NHY · PDBe 4NHY · UniProt Q8N543
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