MolNFT v1 · #20639 · protein
Crystal structure at 1.8 ångström of cdp-D-glucose 4,6- dehydratase from yersinia pseudotuberculosis
1RKX · Cdp-glucose-4,6-dehydratase: “Crystal structure at 1.8 ångström of cdp-D-glucose 4,6- dehydratase from yersinia pseudotuberculosis”. X-ray diffraction, 1 ligand (NAD), 9 pockets (best druggability 0.81). MolNFT v1 #20639 on…
- PDB
- 1RKX
- Type
- protein
- Length
- 1,393 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cdp-glucose-4,6-dehydratase
- EC
- 4.2.1.45
- UniProt
- Q57329
- Ligands
- NAD
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cdp-glucose-4,6-dehydratase (EC 4.2.1.45) | protein | 349 | 49% helix, 14% strand | Q57329 |
| B | Cdp-glucose-4,6-dehydratase (EC 4.2.1.45) | protein | 346 | 50% helix, 14% strand | Q57329 |
| C | Cdp-glucose-4,6-dehydratase (EC 4.2.1.45) | protein | 351 | 50% helix, 14% strand | Q57329 |
| D | Cdp-glucose-4,6-dehydratase (EC 4.2.1.45) | protein | 347 | 50% helix, 14% strand | Q57329 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.81 | 0.92 | 51 | empty |
| 2 | 406 | 0.81 | 0.89 | 59 | empty |
| 3 | 829 | 0.78 | 0.82 | 82 | NAD |
| 4 | 926 | 0.78 | 0.81 | 86 | NAD |
| 5 | 852 | 0.78 | 0.81 | 83 | NAD |
Interfaces
4 interfaces between chains.
- B–D · 1172 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1166 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 884 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 876 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1RKX · Crystal Structure at 1.8 Angstrom of CDP-D-glucose 4,6-dehydratase from Yersinia… · the same entry in another collection · 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 Q57329
- Elsewhere: RCSB PDB 1RKX · PDBe 1RKX · UniProt Q57329
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