Research workbench
Polysulfide reductase with bound menaquinone
Analyse Polysulfide reductase with bound menaquinone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VPW
- 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, MQ7, MO
- Pockets
- 20 · best druggability 0.88
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 | 29% 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
- MQ7 · Menaquinone-7 · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.88 | 0.89 | 141 | MGD, MO |
| 2 | 1027 | 0.88 | 0.90 | 135 | MGD, MO |
| 3 | 531 | 0.82 | 0.88 | 76 | empty |
| 4 | 436 | 0.80 | 0.88 | 46 | empty |
| 5 | 328 | 0.72 | 0.84 | 34 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1879 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1799 Ų buried · 22 hydrogen bonds · protein-protein
- F–G · 1660 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 1629 Ų buried · 36 hydrogen bonds · protein-protein
- C–G · 983 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2VPW · Polysulfide reductase with bound menaqui · 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 Q72LA4
- Every structure of UniProt Q72LA5
- Every structure of UniProt Q72LA6
- Elsewhere: RCSB PDB 2VPW · PDBe 2VPW · UniProt Q72LA4 · UniProt Q72LA5 · UniProt Q72LA6
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