MolNFT v1 · #12368 · protein
The crystal structure of dtdp-D-glucose 4,6-dehydratase (rmlb) from streptococcus suis with dtdp-D-glucose bound
1KER: “The crystal structure of dtdp-D-glucose 4,6-dehydratase (rmlb) from streptococcus suis with dtdp-D-glucose…”. X-ray diffraction, 3 ligands (DAU, NAD, SO4), 9 pockets (best druggability 0.87). MolNFT v1 #12368 on GenesisL1: 3D…
- PDB
- 1KER
- Type
- protein
- Length
- 693 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
- P95780
- Ligands
- DAU, NAD, SO4
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dtdp-D-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 346 | 44% helix, 17% strand | P95780 |
| B | Dtdp-D-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 347 | 43% helix, 17% strand | P95780 |
Ligands and binding sites
- DAU · 2'deoxy-thymidine-5'-diphospho-alpha-D-glucose · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.87 | 0.94 | 63 | DAU, NAD |
| 2 | 434 | 0.86 | 0.94 | 60 | DAU, NAD |
| 3 | 84 | 0.42 | 0.79 | 20 | empty |
| 4 | 108 | 0.41 | 0.76 | 20 | empty |
| 5 | 54 | 0.38 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1358 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1KER · The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis… · the same entry in another collection · chain A against A, TM-score 1.00
- P95780 · AlphaFold monomer V2.0 prediction for dtdp-glucose 4,6-dehydratase (P95780) · a predicted model of the same protein · 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 P95780
- Elsewhere: RCSB PDB 1KER · PDBe 1KER · UniProt P95780
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