Research workbench
Crystal structure of formate dehydrogenase mutant V198I/C256I/P260S/E261P/S381N/S383F from pseudomonas sp. 101
Analyse Crystal structure of formate dehydrogenase mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JX1
- Type
- protein
- Length
- 741 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate dehydrogenase
- EC
- 1.17.1.9
- UniProt
- P33160
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formate dehydrogenase (EC 1.17.1.9) | protein | 374 | 33% helix, 18% strand | P33160 |
| B | Formate dehydrogenase (EC 1.17.1.9) | protein | 367 | 35% helix, 17% strand | P33160 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.69 | 0.82 | 48 | empty |
| 2 | 294 | 0.69 | 0.83 | 39 | empty |
| 3 | 273 | 0.54 | 0.76 | 40 | empty |
| 4 | 93 | 0.42 | 0.77 | 14 | empty |
| 5 | 95 | 0.40 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3921 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 6JX1 · Crystal structure of Formate dehydrogenase mutant V198I/C256I/P260S/E261P/S381N/S383F… · the same entry in another collection · chain A against A, TM-score 1.00
- P33160 · AlphaFold monomer V2.0 prediction for formate dehydrogenase (P33160) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P33160
- Elsewhere: RCSB PDB 6JX1 · PDBe 6JX1 · UniProt P33160
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