MolNFT v1 · #161627 · protein
Di-tert-butyl polysulfide inhibited sulfur oxygenase reductase
6QKA · Sulfur OXYGENASE/REDUCTASE: “Di-tert-butyl polysulfide inhibited sulfur oxygenase reductase”. X-ray diffraction, 1 ligand (FE), 20 pockets (best druggability 0.88). MolNFT v1 #161627 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6QKA
- Type
- protein
- Length
- 1,842 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfur OXYGENASE/REDUCTASE
- EC
- 1.13.11.55
- UniProt
- P29082
- Ligands
- FE
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Sulfur OXYGENASE/REDUCTASE (EC 1.13.11.55) | protein | 307 | 36% helix, 31% strand | P29082 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.88 | 0.90 | 83 | empty |
| 2 | 882 | 0.88 | 0.90 | 81 | empty |
| 3 | 1196 | 0.88 | 0.89 | 129 | empty |
| 4 | 206 | 0.83 | 0.96 | 39 | FE |
| 5 | 208 | 0.83 | 0.96 | 39 | FE |
Interfaces
8 interfaces between chains.
- A–B · 2430 Ų buried · 51 hydrogen bonds · protein-protein
- D–F · 2412 Ų buried · 48 hydrogen bonds · protein-protein
- C–E · 2371 Ų buried · 52 hydrogen bonds · protein-protein
- B–E · 1286 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 1283 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (oxidation, nonstandard).
Compared structures
- 6QKA · Di-tert-butyl Polysulfide inhibited sulfur oxygenase reductase · the same entry in another collection · chain A against A, TM-score 1.00
- P29082 · AlphaFold monomer V2.0 prediction for sulfur OXYGENASE/REDUCTASE (P29082) · a predicted model of the same protein · 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 P29082
- Elsewhere: RCSB PDB 6QKA · PDBe 6QKA · UniProt P29082
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