MolNFT v1 · #140470 · protein
FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase prha- V150L/A232S/M241V in complex with berkeleyone a
5YBT: “FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase prha- V150L/A232S/M241V in complex with berkeleyone a”. X-ray diffraction, 3 ligands (AKG, 8TC, FE), 6 pockets (best druggability 0.80). MolNFT v1 #140470 on GenesisL1: 3D structure…
- PDB
- 5YBT
- Type
- protein
- Length
- 588 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prha
- UniProt
- A0A1E1FFL0
- Ligands
- AKG, 8TC, FE
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prha | protein | 293 | 27% helix, 23% strand | A0A1E1FFL0 |
| B | Prha | protein | 295 | 26% helix, 25% strand | A0A1E1FFL0 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- 8TC · berkeleyone A · 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.80 | 0.86 | 74 | FE, AKG, 8TC |
| 2 | 502 | 0.80 | 0.87 | 54 | FE, AKG, 8TC |
| 3 | 51 | 0.71 | 0.98 | 22 | empty |
| 4 | 61 | 0.30 | 0.75 | 15 | empty |
| 5 | 52 | 0.28 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2075 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5YBT · Fe(II)/(alpha)ketoglutarate-dependent dioxygenase PrhA-V150L/A232S/M241V 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 5YBT · PDBe 5YBT · UniProt A0A1E1FFL0
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