Research workbench
Crystal structure of aspartate kinase from corynebacterium glutamicum in complex with lysine and threonine
Analyse Crystal structure of aspartate kinase from corynebacterium glutamicum in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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