MolNFT v1 · #57545 · protein
Crystal structure of aspartate kinase from corynebacterium glutamicum in complex with lysine and threonine
3AAW · Aspartokinase: “Crystal structure of aspartate kinase from corynebacterium glutamicum in complex with lysine and threonine”. X-ray diffraction, 2 ligands (THR, LYS), 14 pockets (best druggability 0.64). MolNFT v1 #57545 on…
- PDB
- 3AAW
- Type
- protein
- Length
- 1,098 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartokinase; Aspartokinase lysc beta subunit
- EC
- 2.7.2.4
- UniProt
- P26512, Q93C54
- Ligands
- THR, LYS
- Pockets
- 14 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartokinase (EC 2.7.2.4) | protein | 387 | 39% helix, 25% strand | P26512 |
| B | Aspartokinase lysc beta subunit (EC 2.7.2.4) | protein | 160 | 32% helix, 35% strand | Q93C54 |
| C | Aspartokinase (EC 2.7.2.4) | protein | 392 | 40% helix, 24% strand | P26512 |
| D | Aspartokinase lysc beta subunit (EC 2.7.2.4) | protein | 159 | 34% helix, 36% strand | Q93C54 |
Ligands and binding sites
- THR · Threonine · ligand · 4 copies · chains A, B, C, D
- LYS · Lysine · ligand · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.64 | 0.77 | 47 | LYS |
| 2 | 258 | 0.61 | 0.80 | 41 | empty |
| 3 | 418 | 0.59 | 0.75 | 38 | empty |
| 4 | 203 | 0.58 | 0.80 | 34 | empty |
| 5 | 214 | 0.58 | 0.80 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2930 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 2885 Ų buried · 48 hydrogen bonds · protein-protein
- A–C · 1369 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3AAW · Crystal structure of aspartate kinase from Corynebacterium glutamicum in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P26512 · AlphaFold monomer V2.0 prediction for aspartokinase (P26512) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P26512
- Every structure of UniProt Q93C54
- Elsewhere: RCSB PDB 3AAW · PDBe 3AAW · UniProt P26512 · UniProt Q93C54
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