MolNFT v1 · #122494 · protein
WELO5 bound to FE(II), cl, 2-oxoglutarate, and 12-epifischerindole U
5IQT: “WELO5 bound to FE(II), cl, 2-oxoglutarate, and 12-epifischerindole U”. X-ray diffraction, 4 ligands (AKG, 6CU, FE2), 5 pockets (best druggability 0.81). MolNFT v1 #122494 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IQT
- Type
- protein
- Length
- 837 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- WELO5
- UniProt
- A0A067YX61
- Ligands
- AKG, 6CU, FE2, CL
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | WELO5 | protein | 280 | 33% helix, 27% strand | A0A067YX61 |
| C | WELO5 | protein | 277 | 34% helix, 27% strand | A0A067YX61 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 3 copies · chains A, B, C
- 6CU · (6aS,9R,10R,10aS)-9-ethyl-10-isocyano-6,6,9-trimethyl-5,6,6a,7,8,9,10,10a-octahydroindeno[2,1-b]indole · ligand · 2 copies · chains A, B
- FE2 · Fe (II) ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.81 | 0.82 | 99 | FE2, CL, AKG, 6CU |
| 2 | 432 | 0.71 | 0.82 | 43 | FE2, CL, AKG, 6CU |
| 3 | 463 | 0.71 | 0.81 | 44 | FE2, CL, AKG |
| 4 | 313 | 0.62 | 0.79 | 36 | empty |
| 5 | 292 | 0.59 | 0.78 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–B · 661 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 253 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 31 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5IQT · WelO5 bound to Fe(II), Cl, 2-oxoglutarate, and 12-epifischerindole U · 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 A0A067YX61
- Elsewhere: RCSB PDB 5IQT · PDBe 5IQT · UniProt A0A067YX61
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