MolNFT v1 · #122496 · protein
WELO5 bound to fe, cl, 2-oxoglutarate, 12-epifischerindole U, and nitric oxide
5IQV: “WELO5 bound to fe, cl, 2-oxoglutarate, 12-epifischerindole U, and nitric oxide”. X-ray diffraction, 5 ligands (AKG, 6CU, FE2), 9 pockets (best druggability 0.82). MolNFT v1 #122496 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5IQV
- Type
- protein
- Length
- 827 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- WELO5
- UniProt
- A0A067YX61
- Ligands
- AKG, 6CU, FE2, CL, NO
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | WELO5 | protein | 277 | 33% helix, 27% strand | A0A067YX61 |
| B | WELO5 | protein | 276 | 34% helix, 28% strand | A0A067YX61 |
| C | WELO5 | protein | 274 | 33% helix, 28% 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 · 3 copies · chains A, B, C
- FE2 · Fe (II) ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- NO · Nitric oxide · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.82 | 0.92 | 40 | FE2, AKG, 6CU, CL, NO |
| 2 | 330 | 0.81 | 0.91 | 39 | FE2, AKG, 6CU, CL, NO |
| 3 | 340 | 0.69 | 0.82 | 39 | FE2, AKG, 6CU, CL |
| 4 | 294 | 0.63 | 0.80 | 35 | empty |
| 5 | 345 | 0.54 | 0.74 | 53 | empty |
Interfaces
3 interfaces between chains.
- B–C · 722 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 718 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 60 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5IQV · WelO5 bound to Fe, Cl, 2-oxoglutarate, 12-epifischerindole U, and nitric oxide · 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 5IQV · PDBe 5IQV · UniProt A0A067YX61
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