MolNFT v1 · #163804 · protein
W-formate dehydrogenase from desulfovibrio vulgaris - oxidized form
6SDR · Formate dehydrogenase, alpha subunit, selenocysteine…: “W-formate dehydrogenase from desulfovibrio vulgaris - oxidized form”. X-ray diffraction, 4 ligands (SF4, MGD, W), 13 pockets (best druggability 0.89). MolNFT v1 #163804 on…
- PDB
- 6SDR
- Type
- protein
- Length
- 1,177 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, H2S
- Pockets
- 13 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formate dehydrogenase, alpha subunit, selenocysteine- containing (EC 1.2.1.2) | protein | 963 | 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
- H2S · Hydrosulfuric acid · ion · chains A
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.89 | 0.96 | 83 | MGD, H2S, W |
| 2 | 919 | 0.75 | 0.78 | 85 | GOL |
| 3 | 285 | 0.66 | 0.82 | 46 | empty |
| 4 | 59 | 0.49 | 0.85 | 21 | GOL |
| 5 | 99 | 0.44 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2176 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6SDR · W-formate dehydrogenase from Desulfovibrio vulgaris - Oxidized 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 6SDR · PDBe 6SDR · UniProt Q72EJ1 · UniProt Q72EJ0
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