MolNFT v1 · #52066 · protein
Polysulfide reductase with bound quinone (UQ1)
2VPX · Thiosulfate reductase: “Polysulfide reductase with bound quinone (UQ1)”. X-ray diffraction, 4 ligands (SF4, MGD, UQ1), 20 pockets (best druggability 0.89). MolNFT v1 #52066 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2VPX
- Type
- protein
- Length
- 2,354 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiosulfate reductase; Nrfc protein; Hypothetical membrane spanning protein
- UniProt
- Q72LA4, Q72LA5, Q72LA6
- Ligands
- SF4, MGD, UQ1, MO
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Thiosulfate reductase | protein | 734 | 30% helix, 17% strand | Q72LA4 |
| B, F | Nrfc protein | protein | 193 | 18% helix, 23% strand | Q72LA5 |
| C, G | Hypothetical membrane spanning protein | protein | 250 | 67% helix, 1% strand | Q72LA6 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 10 copies · chains A, B, E, F
- MGD · 2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide · ligand · 4 copies · chains A, E
- UQ1 · Ubiquinone-1 · ligand · 2 copies · chains B, C, F, G
- MO · Molybdenum atom · metal · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.89 | 0.97 | 76 | MGD, MO |
| 2 | 1032 | 0.88 | 0.89 | 134 | MGD, MO |
| 3 | 504 | 0.82 | 0.89 | 77 | empty |
| 4 | 419 | 0.80 | 0.88 | 46 | empty |
| 5 | 1148 | 0.76 | 0.78 | 81 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1866 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1796 Ų buried · 23 hydrogen bonds · protein-protein
- F–G · 1650 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 1622 Ų buried · 37 hydrogen bonds · protein-protein
- C–G · 974 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2VPX · Polysulfide reductase with bound qui (UQ1) · the same entry in another collection · chain B against B, 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 Q72LA4
- Every structure of UniProt Q72LA5
- Every structure of UniProt Q72LA6
- Elsewhere: RCSB PDB 2VPX · PDBe 2VPX · UniProt Q72LA4 · UniProt Q72LA5 · UniProt Q72LA6
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