Research workbench
Structure of cdp-D-glucose 4,6-dehydratase from salmonella typhi
Analyse Structure of cdp-D-glucose 4,6-dehydratase from salmonella typhi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WVG
- Type
- protein
- Length
- 702 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cdp-glucose 4,6-dehydratase
- EC
- 4.2.1.45
- UniProt
- P26397
- Ligands
- APR, CXY
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cdp-glucose 4,6-dehydratase (EC 4.2.1.45) | protein | 352 | 49% helix, 15% strand | P26397 |
| B | Cdp-glucose 4,6-dehydratase (EC 4.2.1.45) | protein | 350 | 48% helix, 15% strand | P26397 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · 2 copies · chains A, B
- CXY · Cytidine-5'-diphospho-beta-D-xylose · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.84 | 0.89 | 72 | APR, CXY |
| 2 | 840 | 0.78 | 0.81 | 79 | APR |
| 3 | 291 | 0.60 | 0.79 | 38 | empty |
| 4 | 235 | 0.51 | 0.76 | 26 | empty |
| 5 | 68 | 0.28 | 0.73 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1152 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1WVG · Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi · the same entry in another collection · chain A against A, TM-score 1.00
- P26397 · AlphaFold monomer V2.0 prediction for cdp-glucose 4,6-dehydratase (P26397) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P26397
- Elsewhere: RCSB PDB 1WVG · PDBe 1WVG · UniProt P26397
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