MolNFT v1 · #140463 · protein
FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase prha
5YBM: “FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase prha”. X-ray diffraction, 4 pockets (best druggability 0.81). MolNFT v1 #140463 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YBM
- Type
- protein
- Length
- 586 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prha
- UniProt
- A0A1E1FFL0
- Pockets
- 4 · 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 | 296 | 28% helix, 23% strand | A0A1E1FFL0 |
| B | Prha | protein | 290 | 28% helix, 23% strand | A0A1E1FFL0 |
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 | 562 | 0.81 | 0.87 | 59 | empty |
| 2 | 420 | 0.68 | 0.80 | 49 | empty |
| 3 | 85 | 0.37 | 0.76 | 22 | empty |
| 4 | 52 | 0.36 | 0.80 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1977 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5YBM · Fe(II)/(alpha)ketoglutarate-dependent dioxygenase PrhA · 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 5YBM · PDBe 5YBM · UniProt A0A1E1FFL0
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