MolNFT v1 · #152428 · protein
Crystal structure of phosphite dehydrogenase mutant I151R/P176E from ralstonia sp. 4506 in complex with non-natural cofactor nicotinamide cytosine dinucleotide
6IH5: “Crystal structure of phosphite dehydrogenase mutant I151R/P176E from ralstonia sp. 4506 in complex with…”. X-ray diffraction, 1 ligand (A7R), 7 pockets (best druggability 0.82). MolNFT v1 #152428 on GenesisL1: 3D structure, binding…
- PDB
- 6IH5
- 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
- 7 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphite dehydrogenase | protein | 329 | 37% 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 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.82 | 0.85 | 88 | empty |
| 2 | 311 | 0.74 | 0.86 | 37 | A7R |
| 3 | 123 | 0.62 | 0.87 | 30 | empty |
| 4 | 93 | 0.52 | 0.83 | 20 | empty |
| 5 | 107 | 0.50 | 0.81 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1276 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6IH5 · Crystal structure of Phosphite Dehydrogenase mutant I151R/P176E from Ralstonia sp. 4506… · 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 6IH5 · PDBe 6IH5 · UniProt G4XDR8
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