Research workbench
Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana complexed with PLP-DAP: an external aldimine mimic
Analyse Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EI6
- Type
- protein
- Length
- 821 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Arabidopsis thaliana
- Molecule
- LL-diaminopimelate aminotransferase
- EC
- 2.6.1.83
- UniProt
- Q93ZN9
- Ligands
- PL4, SO4
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.9 · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LL-diaminopimelate aminotransferase (EC 2.6.1.83) | protein | 410 | 45% helix, 14% strand | Q93ZN9 |
| B | LL-diaminopimelate aminotransferase (EC 2.6.1.83) | protein | 411 | 44% helix, 14% strand | Q93ZN9 |
Ligands and binding sites
- PL4 · (2S,6S)-2-amino-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]heptanedioic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.71 | 0.98 | 19 | empty |
| 2 | 521 | 0.70 | 0.80 | 76 | GOL, PL4 |
| 3 | 338 | 0.70 | 0.83 | 49 | PL4 |
| 4 | 212 | 0.67 | 0.85 | 30 | empty |
| 5 | 205 | 0.65 | 0.84 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 3942 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 3EI6 · Crystal structure of ll-diaminopimelate aminotransferase from arabidopsis thaliana… · the same entry in another collection · chain A against A, TM-score 1.00
- Q93ZN9 · AlphaFold monomer V2.0 prediction for ll-diaminopimelate aminotransferase, chloroplastic… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q93ZN9
- Elsewhere: RCSB PDB 3EI6 · PDBe 3EI6 · UniProt Q93ZN9
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