Research workbench
Crystal structure of ll-diaminopimelate aminotransferase from arabidopsis thaliana complexed with L-malate ion
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
- 2Z1Z
- Type
- protein
- Length
- 816 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
- O81885
- Ligands
- PLP, MLT
- Pockets
- 8 · best druggability 0.77
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 | 408 | 45% helix, 14% strand | O81885 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.77 | 0.99 | 21 | empty |
| 2 | 383 | 0.69 | 0.82 | 54 | MLT, PLP |
| 3 | 209 | 0.69 | 0.86 | 27 | empty |
| 4 | 389 | 0.68 | 0.80 | 49 | PLP |
| 5 | 200 | 0.66 | 0.85 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 3955 Ų buried · 60 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2Z1Z · Crystal structure of LL-Diaminopimelate Aminotransferase from Arabidopsis thaliana… · the same entry in another collection · chain B against B, 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 O81885
- Elsewhere: RCSB PDB 2Z1Z · PDBe 2Z1Z · UniProt O81885
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