MolNFT v1 · #140462 · protein
FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase ause
5YBL · Multifunctional dioxygenase ause: “FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase ause”. X-ray diffraction, 2 ligands (AKG, MN), 11 pockets (best druggability 0.72). MolNFT v1 #140462 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YBL
- Type
- protein
- Length
- 1,049 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multifunctional dioxygenase ause
- EC
- 1.14.11.-
- UniProt
- Q5AR34
- Ligands
- AKG, MN
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multifunctional dioxygenase ause (EC 1.14.11.-) | protein | 272 | 30% helix, 24% strand | Q5AR34 |
| B | Multifunctional dioxygenase ause (EC 1.14.11.-) | protein | 273 | 27% helix, 26% strand | Q5AR34 |
| C | Multifunctional dioxygenase ause (EC 1.14.11.-) | protein | 252 | 29% helix, 25% strand | Q5AR34 |
| D | Multifunctional dioxygenase ause (EC 1.14.11.-) | protein | 252 | 31% helix, 24% strand | Q5AR34 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, C
- MN · Manganese (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
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.72 | 0.81 | 66 | MN |
| 2 | 369 | 0.66 | 0.80 | 42 | MN, AKG |
| 3 | 345 | 0.65 | 0.80 | 41 | MN, AKG |
| 4 | 466 | 0.64 | 0.77 | 51 | empty |
| 5 | 350 | 0.63 | 0.79 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1626 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1591 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 546 Ų buried · 11 hydrogen bonds · 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 Q5AR34
- Elsewhere: RCSB PDB 5YBL · PDBe 5YBL · UniProt Q5AR34
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