MolNFT v1 · #34861 · protein
Crystal structure of the regulatory subunit of aspartate kinase from thermus flavus
2DT9 · Aspartokinase: “Crystal structure of the regulatory subunit of aspartate kinase from thermus flavus”. X-ray diffraction, 1 ligand (THR), 4 pockets (best druggability 0.48). MolNFT v1 #34861 on GenesisL1: 3D structure, binding sites…
- PDB
- 2DT9
- Type
- protein
- Length
- 306 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartokinase
- EC
- 2.7.2.4
- UniProt
- P61489
- Ligands
- THR
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartokinase (EC 2.7.2.4) | protein | 153 | 39% helix, 35% strand | P61489 |
Ligands and binding sites
- THR · Threonine · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.48 | 0.81 | 21 | ACT |
| 2 | 66 | 0.38 | 0.79 | 17 | empty |
| 3 | 79 | 0.37 | 0.77 | 21 | empty |
| 4 | 68 | 0.36 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1954 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2DT9 · Crystal structure of the regulatory subunit of aspartate kinase from Thermus flavus · the same entry in another collection · chain A against A, TM-score 1.00
- P61489 · AlphaFold monomer V2.0 prediction for aspartokinase (P61489) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P61489
- Elsewhere: RCSB PDB 2DT9 · PDBe 2DT9 · UniProt P61489
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