MolNFT v1 · #62524 · protein
Crystal structure of ll-diaminopimelate aminotransferase from arabidopsis thaliana complexed with plp-glu: an external aldimine mimic
3EI5: “Crystal structure of ll-diaminopimelate aminotransferase from arabidopsis thaliana complexed with plp-glu: an…”. X-ray diffraction, 2 ligands (PGU, SO4), 11 pockets (best druggability 0.74). MolNFT v1 #62524 on GenesisL1: 3D…
- PDB
- 3EI5
- Type
- protein
- Length
- 818 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
- PGU, SO4
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 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 | 408 | 45% helix, 14% strand | Q93ZN9 |
| B | Ll-diaminopimelate aminotransferase (EC 2.6.1.83) | protein | 410 | 44% helix, 14% strand | Q93ZN9 |
Ligands and binding sites
- PGU · N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.74 | 0.99 | 20 | empty |
| 2 | 497 | 0.70 | 0.80 | 62 | PGU |
| 3 | 365 | 0.69 | 0.82 | 53 | PGU |
| 4 | 224 | 0.67 | 0.84 | 30 | empty |
| 5 | 214 | 0.66 | 0.85 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 3967 Ų buried · 67 hydrogen bonds · protein-protein
Compared structures
- 3EI5 · 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 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 Q93ZN9
- Elsewhere: RCSB PDB 3EI5 · PDBe 3EI5 · UniProt Q93ZN9
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