MolNFT v1 · #33219 · protein
Crystal structure of arabidopsis thaliana aspartate kinase complexed with lysine and S-adenosylmethionine
2CDQ · Aspartokinase: “Crystal structure of arabidopsis thaliana aspartate kinase complexed with lysine and S-adenosylmethionine”. X-ray diffraction, 2 ligands (LYS, SAM), 13 pockets (best druggability 0.72). MolNFT v1 #33219 on GenesisL1…
- PDB
- 2CDQ
- Type
- protein
- Length
- 940 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartokinase
- EC
- 2.7.2.4
- UniProt
- Q9LYU8
- Ligands
- LYS, SAM
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartokinase (EC 2.7.2.4) | protein | 470 | 44% helix, 22% strand | Q9LYU8 |
Ligands and binding sites
- LYS · Lysine · ligand · 4 copies · chains A, B
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- TAR · D(-)-tartaric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.72 | 0.99 | 26 | LYS |
| 2 | 54 | 0.72 | 0.98 | 27 | LYS |
| 3 | 829 | 0.71 | 0.77 | 65 | LYS |
| 4 | 761 | 0.71 | 0.77 | 47 | LYS |
| 5 | 152 | 0.52 | 0.79 | 21 | SAM |
Interfaces
1 interface between chains.
- A–B · 3110 Ų buried · 57 hydrogen bonds · protein-protein
Compared structures
- 2CDQ · Crystal structure of Arabidopsis thaliana aspartate kinase complexed with lysine and S… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9LYU8 · AlphaFold monomer V2.0 prediction for aspartokinase 1, chloroplastic (Q9LYU8) · 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 Q9LYU8
- Elsewhere: RCSB PDB 2CDQ · PDBe 2CDQ · UniProt Q9LYU8
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