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The crystal structure of dtdp-D-glucose 4,6-dehydratase (rmlb) from streptococcus suis with dtdp-xylose bound
Analyse The crystal structure of dtdp-D-glucose 4,6-dehydratase (rmlb) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KEP
- Type
- protein
- Length
- 692 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
- NAD, TDX, SO4
- Pockets
- 8 · 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 | 45% helix, 17% strand | P95780 |
| B | Dtdp-D-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 346 | 44% helix, 17% strand | P95780 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- TDX · Thymidine-5'-diphospho-beta-D-xylose · 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
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.87 | 0.93 | 63 | NAD, TDX |
| 2 | 512 | 0.87 | 0.93 | 64 | NAD, TDX |
| 3 | 152 | 0.46 | 0.77 | 27 | empty |
| 4 | 111 | 0.45 | 0.78 | 24 | empty |
| 5 | 124 | 0.44 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1384 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1KEP · 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 1KEP · PDBe 1KEP · UniProt P95780
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