Research workbench
Crystal structure of the prephenate aminotransferase from arabidopsis thaliana
Analyse Crystal structure of the prephenate aminotransferase from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F5V
- Type
- protein
- Length
- 1,606 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional aspartate aminotransferase and GLUTAMATE/ASPARTATE-prephenate…
- EC
- 2.6.1.1, 2.6.1.78, 2.6.1.79
- UniProt
- Q9SIE1
- Ligands
- PLP, NA
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional aspartate aminotransferase and GLUTAMATE/ASPARTATE-prephenate aminotransferase (EC 2.6.1.1, 2.6.1.78, 2.6.1.79) | protein | 401 | 46% helix, 16% strand | Q9SIE1 |
| B | Bifunctional aspartate aminotransferase and GLUTAMATE/ASPARTATE-prephenate aminotransferase (EC 2.6.1.1, 2.6.1.78, 2.6.1.79) | protein | 403 | 46% helix, 15% strand | Q9SIE1 |
| C | Bifunctional aspartate aminotransferase and GLUTAMATE/ASPARTATE-prephenate aminotransferase (EC 2.6.1.1, 2.6.1.78, 2.6.1.79) | protein | 399 | 46% helix, 16% strand | Q9SIE1 |
| D | Bifunctional aspartate aminotransferase and GLUTAMATE/ASPARTATE-prephenate aminotransferase (EC 2.6.1.1, 2.6.1.78, 2.6.1.79) | protein | 403 | 45% helix, 16% strand | Q9SIE1 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, B
- CIT · Citric acid · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.77 | 0.98 | 23 | empty |
| 2 | 913 | 0.76 | 0.79 | 72 | PLP, CIT |
| 3 | 871 | 0.74 | 0.78 | 77 | PLP, CIT |
| 4 | 850 | 0.74 | 0.79 | 76 | PLP, CIT |
| 5 | 725 | 0.73 | 0.79 | 76 | PLP |
Interfaces
4 interfaces between chains.
- C–D · 2847 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 2840 Ų buried · 55 hydrogen bonds · protein-protein
- A–C · 410 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 35 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6F5V · Crystal structure of the prephenate aminotransferase from Arabidopsis thaliana · the same entry in another collection · chain D against D, TM-score 1.00
- Q9SIE1 · AlphaFold monomer V2.0 prediction for bifunctional aspartate aminotransferase and… · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q9SIE1
- Elsewhere: RCSB PDB 6F5V · PDBe 6F5V · UniProt Q9SIE1
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