Research workbench
FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase prha in complex with preaustinoid A1
Analyse FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase prha in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YBO
- Type
- protein
- Length
- 579 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prha
- UniProt
- A0A1E1FFL0
- Ligands
- AKG, 8SX, FE
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prha | protein | 294 | 29% helix, 23% strand | A0A1E1FFL0 |
| B | Prha | protein | 285 | 28% helix, 22% strand | A0A1E1FFL0 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- 8SX · preaustinoid A1 · ligand · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.81 | 0.87 | 59 | FE, AKG, 8SX |
| 2 | 192 | 0.70 | 0.87 | 42 | empty |
| 3 | 286 | 0.65 | 0.81 | 32 | FE, AKG |
| 4 | 78 | 0.30 | 0.73 | 18 | empty |
| 5 | 62 | 0.28 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1997 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5YBO · Fe(II)/(alpha)ketoglutarate-dependent dioxygenase PrhA in complex with preaustinoid A1 · the same entry in another collection · 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 A0A1E1FFL0
- Elsewhere: RCSB PDB 5YBO · PDBe 5YBO · UniProt A0A1E1FFL0
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