MolNFT v1 · #62527 · protein
Crystal structure of K270N variant of ll-diaminopimelate aminotransferase from arabidopsis thaliana complexed with ll-dap: external aldimine form
3EI8: “Crystal structure of K270N variant of ll-diaminopimelate aminotransferase from arabidopsis thaliana complexed…”. X-ray diffraction, 3 ligands (PLP, PL5, SO4), 10 pockets (best druggability 0.73). MolNFT v1 #62527 on GenesisL1: 3D…
- PDB
- 3EI8
- Type
- protein
- Length
- 822 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ll-diaminopimelate aminotransferase
- EC
- 2.6.1.83
- UniProt
- Q93ZN9
- Ligands
- PLP, PL5, SO4
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ll-diaminopimelate aminotransferase (EC 2.6.1.83) | protein | 411 | 45% helix, 14% strand | Q93ZN9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A, B
- PL5 · (2S,6S)-2-amino-6-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}heptanedioic acid · ligand · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.73 | 0.99 | 21 | empty |
| 2 | 465 | 0.71 | 0.81 | 66 | PL5 |
| 3 | 377 | 0.70 | 0.82 | 52 | PLP |
| 4 | 235 | 0.68 | 0.85 | 27 | empty |
| 5 | 213 | 0.66 | 0.84 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 3950 Ų buried · 58 hydrogen bonds · protein-protein
Compared structures
- 3EI8 · Crystal structure of K270N variant of LL-diaminopimelate aminotransferase from… · 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 B 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 3EI8 · PDBe 3EI8 · UniProt Q93ZN9
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