MolNFT v1 · #153914 · protein
Crystal structure of formate dehydrogenase mutant C256I/E261P/S381I from pseudomonas sp. 101 in complex with non-natural cofactor nicotinamide cytosine dinucleotide
6JUK: “Crystal structure of formate dehydrogenase mutant C256I/E261P/S381I from pseudomonas sp. 101 in complex with…”. X-ray diffraction, 1 ligand (A7R), 9 pockets (best druggability 0.72). MolNFT v1 #153914 on GenesisL1: 3D structure…
- PDB
- 6JUK
- Type
- protein
- Length
- 748 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
- Ligands
- A7R
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, 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 · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.72 | 0.80 | 54 | A7R |
| 2 | 444 | 0.72 | 0.82 | 47 | A7R |
| 3 | 214 | 0.49 | 0.76 | 41 | empty |
| 4 | 115 | 0.46 | 0.78 | 14 | empty |
| 5 | 110 | 0.44 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3938 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 6JUK · Crystal structure of Formate dehydrogenase mutant C256I/E261P/S381I from Pseudomonas sp.… · 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 6JUK · PDBe 6JUK · UniProt P33160
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