Research workbench
Tungsten containing formate dehydrogenase from desulfovibrio gigas
Analyse Tungsten containing formate dehydrogenase from desulfovibrio gigas in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H0H
- Type
- protein
- Length
- 2,382 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate dehydrogenase subunit alpha; Formate dehydrogenase subunit beta
- EC
- 1.2.1.2
- UniProt
- Q934F5, Q8GC87
- Ligands
- SF4, 2MD, MGD, W, CA, UNX
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K | Formate dehydrogenase subunit alpha (EC 1.2.1.2) | protein | 977 | 31% helix, 20% strand | Q934F5 |
| B, L | Formate dehydrogenase subunit beta | protein | 214 | 27% helix, 22% strand | Q8GC87 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 8 copies · chains A, B, K, L
- 2MD · Guanylate-O'-phosphoric acid mono-(2-amino-5,6-dimercapto-4-oxo-3,5,6,7,8A,9,10,10A-octahydro-4H-8-oxa-1,3,9,10-tetraaza-anthracen-7-ylmethyl) ester · ligand · 2 copies · chains A, K
- 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, K
- W · Tungsten ion · metal · 2 copies · chains A, K
- CA · Calcium ion · metal · 2 copies · chains A, K
- UNX · Unknown atom or ion · ion · 2 copies · chains A, K
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains B, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.90 | 0.96 | 101 | W, 2MD, MGD, UNX |
| 2 | 507 | 0.89 | 0.96 | 84 | W, 2MD, MGD, UNX |
| 3 | 942 | 0.73 | 0.77 | 82 | empty |
| 4 | 977 | 0.73 | 0.76 | 83 | empty |
| 5 | 737 | 0.69 | 0.76 | 68 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2112 Ų buried · 44 hydrogen bonds · protein-protein
- K–L · 2078 Ų buried · 43 hydrogen bonds · protein-protein
- B–K · 142 Ų buried · 2 hydrogen bonds · protein-protein
- A–L · 136 Ų buried · 2 hydrogen bonds · protein-protein
- A–K · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1H0H · Tungsten containing Formate Dehydrogenase from Desulfovibrio Gigas · the same entry in another collection · chain A against A, TM-score 1.00
- Q8GC87 · AlphaFold monomer V2.0 prediction for formate dehydrogenase subunit beta (Q8GC87) · a predicted model of the same protein · chain L against A, TM-score 0.99
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 Q934F5
- Every structure of UniProt Q8GC87
- Elsewhere: RCSB PDB 1H0H · PDBe 1H0H · UniProt Q934F5 · UniProt Q8GC87
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