Research workbench
Rdpa dioxygenase holoenzyme
Analyse Rdpa dioxygenase holoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D0O
- Type
- protein
- Length
- 1,117 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase
- EC
- 1.14.11.44
- UniProt
- Q8KSC8
- Ligands
- AKG, CO
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase (EC 1.14.11.44) | protein | 274 | 24% helix, 27% strand | Q8KSC8 |
| B | (R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase (EC 1.14.11.44) | protein | 267 | 25% helix, 28% strand | Q8KSC8 |
| C | (R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase (EC 1.14.11.44) | protein | 287 | 23% helix, 29% strand | Q8KSC8 |
| D | (R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase (EC 1.14.11.44) | protein | 289 | 23% helix, 28% strand | Q8KSC8 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.81 | 0.95 | 41 | CO, AKG |
| 2 | 278 | 0.78 | 0.90 | 47 | AKG |
| 3 | 878 | 0.75 | 0.79 | 98 | empty |
| 4 | 55 | 0.73 | 0.99 | 19 | empty |
| 5 | 50 | 0.71 | 0.98 | 20 | empty |
Interfaces
6 interfaces between chains.
- B–C · 915 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 874 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 640 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 628 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 218 Ų buried · 1 hydrogen bond · 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 Q8KSC8
- Elsewhere: RCSB PDB 6D0O · PDBe 6D0O · UniProt Q8KSC8
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