MolNFT v2 · #222752 · protein
X-ray structure of the NADP-dependent reductase from Campylobacter jejuni responsible for the synthesis of CDP-glucitol in the presence of CDP-glucitol
8V4H · Putative nucleotide sugar dehydratase: “X-ray structure of the NADP-dependent reductase from Campylobacter jejuni responsible for the synthesis of…”. X-ray diffraction at 2.2, 4 ligands (YCX, NA, CL), 4 pockets (best druggability…
- PDB
- 8V4H
- Type
- protein
- Length
- 676 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Campylobacter jejuni
- Molecule
- Putative nucleotide sugar dehydratase
- UniProt
- A0A0U3AP28
- Ligands
- YCX, NA, CL, PO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.2 · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative nucleotide sugar dehydratase | protein | 334 | 46% helix, 19% strand | A0A0U3AP28 |
| B | Putative nucleotide sugar dehydratase | protein | 342 | 44% helix, 18% strand | A0A0U3AP28 |
Ligands and binding sites
- YCX · [[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-2,3,4,5,6-pentakis(oxidanyl)hexyl] hydrogen phosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
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 | 666 | 0.81 | 0.86 | 73 | YCX, CL |
| 2 | 756 | 0.81 | 0.84 | 82 | YCX, PO4 |
| 3 | 79 | 0.41 | 0.79 | 18 | empty |
| 4 | 96 | 0.41 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1567 Ų buried · 8 hydrogen bonds · protein-protein
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 A0A0U3AP28
- Elsewhere: RCSB PDB 8V4H · PDBe 8V4H · UniProt A0A0U3AP28
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