MolNFT v1 · #116940 · protein
Crystal structure of a putative D-erythronate-4-phosphate dehydrogenase from vibrio cholerae
5DT9: “Crystal structure of a putative D-erythronate-4-phosphate dehydrogenase from vibrio cholerae”. X-ray diffraction, 3 ligands (NAD, SO4, CL), 1 pocket (best druggability 0.70). MolNFT v1 #116940 on GenesisL1: 3D structure, binding…
- PDB
- 5DT9
- Type
- protein
- Length
- 379 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Erythronate-4-phosphate dehydrogenase
- EC
- 1.1.1.290
- UniProt
- Q9KQ92
- Ligands
- NAD, SO4, CL
- Pockets
- 1 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Erythronate-4-phosphate dehydrogenase (EC 1.1.1.290) | protein | 379 | 38% helix, 16% strand | Q9KQ92 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- SO4 · Sulfate ion · ion · 10 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.70 | 0.77 | 65 | NAD, SO4, CL |
Compared structures
- 5DT9 · Crystal structure of a putative D-Erythronate-4-Phosphate Dehydrogenase from Vibrio… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KQ92 · AlphaFold monomer V2.0 prediction for erythronate-4-phosphate dehydrogenase (Q9KQ92) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q9KQ92
- Elsewhere: RCSB PDB 5DT9 · PDBe 5DT9 · UniProt Q9KQ92
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