MolNFT v1 · #121392 · protein
Dahp synthase from corynebacterium glutamicum
5HUC · 3-deoxy-D-arabino-heptulosonate 7-phosphate (dahp) synthase: “Dahp synthase from corynebacterium glutamicum”. X-ray diffraction, 4 ligands (PEP, TRP, MN), 6 pockets (best druggability 0.61). MolNFT v1 #121392 on GenesisL1: 3D…
- PDB
- 5HUC
- Type
- protein
- Length
- 449 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-D-arabino-heptulosonate 7-phosphate (dahp) synthase
- UniProt
- Q8NNL5
- Ligands
- PEP, TRP, MN, PO4
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-D-arabino-heptulosonate 7-phosphate (dahp) synthase | protein | 449 | 43% helix, 14% strand | Q8NNL5 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · chains A
- TRP · Tryptophan · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · 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 | 84 | 0.61 | 0.89 | 26 | PEP |
| 2 | 225 | 0.54 | 0.77 | 25 | TRP |
| 3 | 117 | 0.40 | 0.75 | 18 | empty |
| 4 | 106 | 0.33 | 0.72 | 16 | empty |
| 5 | 75 | 0.31 | 0.74 | 16 | empty |
Compared structures
- 5HUC · DAHP synthase from Corynebacterium glutamicum · 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 Q8NNL5
- Elsewhere: RCSB PDB 5HUC · PDBe 5HUC · UniProt Q8NNL5
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