Research workbench
Formate dehydrogenase from Starkeya novella
Analyse Formate dehydrogenase from Starkeya novella in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QZ1
- Type
- protein
- Length
- 1,488 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Starkeya novella DSM 506
- Molecule
- Formate dehydrogenase
- EC
- 1.17.1.9
- UniProt
- D7A8L2
- Ligands
- NA, CL
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.1 · 4 distinct chains · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formate dehydrogenase (EC 1.17.1.9) | protein | 372 | 35% helix, 17% strand | D7A8L2 |
| B | Formate dehydrogenase (EC 1.17.1.9) | protein | 375 | 34% helix, 17% strand | D7A8L2 |
| C | Formate dehydrogenase (EC 1.17.1.9) | protein | 370 | 35% helix, 18% strand | D7A8L2 |
| D | Formate dehydrogenase (EC 1.17.1.9) | protein | 371 | 35% helix, 17% strand | D7A8L2 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, C, D
- CL · Chloride ion · ion · 2 copies · chains B
- GOL · Glycerol · additive · 15 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.83 | 0.85 | 101 | GOL, PEG |
| 2 | 735 | 0.80 | 0.84 | 77 | GOL |
| 3 | 693 | 0.79 | 0.84 | 64 | GOL |
| 4 | 111 | 0.58 | 0.85 | 16 | empty |
| 5 | 95 | 0.56 | 0.86 | 16 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 3966 Ų buried · 64 hydrogen bonds · protein-protein
- C–D · 985 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 611 Ų buried · 2 hydrogen bonds · protein-protein
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 D7A8L2
- Elsewhere: RCSB PDB 7QZ1 · PDBe 7QZ1 · UniProt D7A8L2
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