MolNFT v1 · #12372 · protein
The crystal structure of dtdp-D-glucose 4,6-dehydratase (rmlb) from salmonella enterica serovar typhimurium with thymidine diphosphate bound
1KEW: “The crystal structure of dtdp-D-glucose 4,6-dehydratase (rmlb) from salmonella enterica serovar typhimurium…”. X-ray diffraction, 2 ligands (TYD, NAD), 6 pockets (best druggability 0.87). MolNFT v1 #12372 on GenesisL1: 3D structure…
- PDB
- 1KEW
- Type
- protein
- Length
- 722 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-D-glucose 4,6-dehydratase
- EC
- 4.2.1.46
- UniProt
- P26391
- Ligands
- TYD, NAD
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dtdp-D-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 361 | 48% helix, 17% strand | P26391 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.87 | 0.94 | 67 | TYD, NAD |
| 2 | 460 | 0.86 | 0.94 | 64 | TYD, NAD |
| 3 | 179 | 0.48 | 0.76 | 27 | empty |
| 4 | 166 | 0.46 | 0.76 | 26 | GOL |
| 5 | 67 | 0.32 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1181 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1KEW · The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Salmonella enterica… · the same entry in another collection · chain A against A, TM-score 1.00
- P26391 · AlphaFold monomer V2.0 prediction for dtdp-glucose 4,6-dehydratase (P26391) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P26391
- Elsewhere: RCSB PDB 1KEW · PDBe 1KEW · UniProt P26391
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.