MolNFT v1 · #165766 · protein
Crystal structure of prephenate dehydrogenase tyra from bacillus anthracis in complex with NAD and L-tyrosine
6U60: “Crystal structure of prephenate dehydrogenase tyra from bacillus anthracis in complex with NAD and L-tyrosine”. X-ray diffraction, 3 ligands (TYR, NAD, PO4), 6 pockets (best druggability 0.83). MolNFT v1 #165766 on GenesisL1: 3D…
- PDB
- 6U60
- Type
- protein
- Length
- 730 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prephenate dehydrogenase
- EC
- 1.3.1.12
- UniProt
- Q81P63
- Ligands
- TYR, NAD, PO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prephenate dehydrogenase (EC 1.3.1.12) | protein | 365 | 51% helix, 18% strand | Q81P63 |
Ligands and binding sites
- TYR · Tyrosine · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.83 | 0.84 | 103 | NAD, PO4 |
| 2 | 576 | 0.77 | 0.83 | 69 | empty |
| 3 | 63 | 0.70 | 0.96 | 21 | TYR |
| 4 | 53 | 0.68 | 0.97 | 24 | TYR |
| 5 | 85 | 0.55 | 0.86 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 6526 Ų buried · 82 hydrogen bonds · protein-protein
Compared structures
- 6U60 · Crystal structure of prephenate dehydrogenase tyrA from Bacillus anthracis in complex… · the same entry in another collection · chain B against B, 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 Q81P63
- Elsewhere: RCSB PDB 6U60 · PDBe 6U60 · UniProt Q81P63
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