MolNFT v1 · #136623 · protein
Crystal structure of prephenate dehydrogenase tyra from bacillus anthracis in complex with L-tyrosine
5UYY: “Crystal structure of prephenate dehydrogenase tyra from bacillus anthracis in complex with L-tyrosine”. X-ray diffraction, 1 ligand (TYR), 13 pockets (best druggability 0.84). MolNFT v1 #136623 on GenesisL1: 3D structure, binding…
- PDB
- 5UYY
- Type
- protein
- Length
- 1,476 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prephenate dehydrogenase
- EC
- 1.3.1.12
- UniProt
- Q81P63
- Ligands
- TYR
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Prephenate dehydrogenase (EC 1.3.1.12) | protein | 373 | 51% helix, 17% strand | Q81P63 |
| B, D | Prephenate dehydrogenase (EC 1.3.1.12) | protein | 365 | 51% helix, 16% strand | Q81P63 |
Ligands and binding sites
- TYR · Tyrosine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1155 | 0.84 | 0.86 | 142 | empty |
| 2 | 1101 | 0.82 | 0.83 | 110 | empty |
| 3 | 83 | 0.73 | 0.96 | 31 | TYR |
| 4 | 53 | 0.69 | 0.97 | 25 | TYR |
| 5 | 52 | 0.68 | 0.97 | 23 | TYR |
Interfaces
5 interfaces between chains.
- A–B · 6509 Ų buried · 65 hydrogen bonds · protein-protein
- C–D · 6482 Ų buried · 73 hydrogen bonds · protein-protein
- B–C · 221 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 166 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 159 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5UYY · Crystal structure of prephenate dehydrogenase tyrA from Bacillus anthracis in complex… · 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 Q81P63
- Elsewhere: RCSB PDB 5UYY · PDBe 5UYY · UniProt Q81P63
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