Research workbench
Crystal structure of a putative formate dehydrogenase from pyrobaculum aerophilum
Analyse Crystal structure of a putative formate dehydrogenase from pyrobaculum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QP8
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate dehydrogenase
- UniProt
- Q8ZXP5
- Ligands
- NDP
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Formate dehydrogenase | protein | 301 | 33% helix, 14% strand | Q8ZXP5 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.73 | 0.83 | 49 | empty |
| 2 | 465 | 0.72 | 0.82 | 50 | NDP |
| 3 | 128 | 0.48 | 0.79 | 24 | empty |
| 4 | 111 | 0.47 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2273 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1QP8 · Crystal structure of a putative formate dehydrogenase from pyrobaculum aerophilum · 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 Q8ZXP5
- Elsewhere: RCSB PDB 1QP8 · PDBe 1QP8 · UniProt Q8ZXP5
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