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Crystal structure of Formate dehydrogenase mutant V198I/C256I/P260S/E261P/S381N/S383F from Pseudomonas sp. 101in complex with non-natural cofactor Nicotinamide Cytosine Dinucleotide
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
- 6JUJ
- Type
- protein
- Length
- 755 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.183
- Source
- Pseudomonas sp. 101
- Molecule
- Formate dehydrogenase
- EC
- 1.17.1.9
- UniProt
- P33160
- Ligands
- A7R
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.183 · 2 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formate dehydrogenase (EC 1.17.1.9) | protein | 381 | 36% helix, 17% strand | P33160 |
| B | Formate dehydrogenase (EC 1.17.1.9) | protein | 374 | 35% helix, 17% strand | P33160 |
Ligands and binding sites
- A7R · [[(2S,3S,4R,5S)-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3S,4R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
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 | 887 | 0.76 | 0.79 | 75 | A7R, GOL |
| 2 | 480 | 0.70 | 0.80 | 52 | A7R |
| 3 | 221 | 0.51 | 0.76 | 39 | GOL |
| 4 | 123 | 0.46 | 0.77 | 15 | empty |
| 5 | 106 | 0.45 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3901 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 6JUJ · 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 0.97
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 6JUJ · PDBe 6JUJ · UniProt P33160
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