MolNFT v1 · #152426 · protein
Crystal structure of phosphite dehydrogenase from ralstonia sp. 4506 in complex with non-natural cofactor nicotinamide cytosine dinucleotide
6IH3: “Crystal structure of phosphite dehydrogenase from ralstonia sp. 4506 in complex with non-natural cofactor…”. X-ray diffraction, 1 ligand (A7R), 4 pockets (best druggability 0.84). MolNFT v1 #152426 on GenesisL1: 3D structure…
- PDB
- 6IH3
- Type
- protein
- Length
- 658 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphite dehydrogenase
- UniProt
- G4XDR8
- Ligands
- A7R
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphite dehydrogenase | protein | 329 | 39% helix, 16% strand | G4XDR8 |
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 · 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 | 983 | 0.84 | 0.85 | 106 | empty |
| 2 | 424 | 0.75 | 0.84 | 48 | A7R |
| 3 | 62 | 0.48 | 0.85 | 15 | empty |
| 4 | 70 | 0.46 | 0.83 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1258 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6IH3 · Crystal structure of Phosphite Dehydrogenase from Ralstonia sp. 4506 in complex with… · 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 G4XDR8
- Elsewhere: RCSB PDB 6IH3 · PDBe 6IH3 · UniProt G4XDR8
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