Research workbench
W-formate dehydrogenase from desulfovibrio vulgaris - formate reduced form
Analyse W-formate dehydrogenase from desulfovibrio vulgaris - formate reduced form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SDV
- Type
- protein
- Length
- 1,181 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate dehydrogenase, alpha subunit, selenocysteine- CONTAINING,FORMATE dehydrogenase…
- EC
- 1.2.1.2
- UniProt
- Q72EJ1, Q72EJ0
- Ligands
- SF4, MGD, W, NO3, H2S
- Pockets
- 13 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formate dehydrogenase, alpha subunit, selenocysteine- CONTAINING,FORMATE dehydrogenase, alpha subunit, selenocysteine- CONTAINING,W-formate dehydrogenase - alpha subunit (EC 1.2.1.2) | protein | 967 | 31% helix, 20% strand | Q72EJ1 |
| B | Formate dehydrogenase, beta subunit, putative | protein | 214 | 29% helix, 21% strand | Q72EJ0 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B
- 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 · 2 copies · chains A
- W · Tungsten ion · metal · chains A
- NO3 · Nitrate ion · ion · 2 copies · chains A
- H2S · Hydrosulfuric acid · ion · chains A
- GOL · Glycerol · additive · 10 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.89 | 0.96 | 82 | MGD, W, H2S |
| 2 | 949 | 0.74 | 0.77 | 92 | GOL |
| 3 | 291 | 0.71 | 0.85 | 37 | empty |
| 4 | 204 | 0.56 | 0.79 | 34 | empty |
| 5 | 89 | 0.43 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2122 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6SDV · W-formate dehydrogenase from Desulfovibrio vulgaris - Formate reduced form · 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 Q72EJ1
- Every structure of UniProt Q72EJ0
- Elsewhere: RCSB PDB 6SDV · PDBe 6SDV · UniProt Q72EJ1 · UniProt Q72EJ0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.