MolNFT v1 · #140464 · protein
FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase prha in complex with (ALPHA)KETOGLUTARATE
5YBN: “FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase prha in complex with (ALPHA)KETOGLUTARATE”. X-ray diffraction, 2 ligands (AKG, FE), 4 pockets (best druggability 0.79). MolNFT v1 #140464 on GenesisL1: 3D structure, binding sites…
- PDB
- 5YBN
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prha
- UniProt
- A0A1E1FFL0
- Ligands
- AKG, FE
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prha | protein | 296 | 30% helix, 21% strand | A0A1E1FFL0 |
| B | Prha | protein | 288 | 28% helix, 22% strand | A0A1E1FFL0 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.79 | 0.84 | 69 | FE, AKG |
| 2 | 371 | 0.66 | 0.80 | 44 | FE, AKG |
| 3 | 80 | 0.37 | 0.77 | 23 | empty |
| 4 | 60 | 0.27 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1953 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5YBN · Fe(II)/(alpha)ketoglutarate-dependent dioxygenase PrhA in complex with… · 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 5YBN · PDBe 5YBN · UniProt A0A1E1FFL0
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