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Crystal structure of citrobacter amalonaticus methylaspartate ammonia lyase containing (2S,3S)-3-methylaspartic acid
Analyse Crystal structure of citrobacter amalonaticus methylaspartate ammonia lyase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KKR
- Type
- protein
- Length
- 822 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-methylaspartate ammonia-lyase
- EC
- 4.3.1.2
- UniProt
- O66145
- Ligands
- 2AS, MG
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-methylaspartate ammonia-lyase (EC 4.3.1.2) | protein | 411 | 44% helix, 18% strand | O66145 |
Ligands and binding sites
- 2AS · (2S,3S)-3-methyl-aspartic acid · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.82 | 0.87 | 51 | empty |
| 2 | 1037 | 0.79 | 0.80 | 119 | 2AS |
| 3 | 107 | 0.37 | 0.74 | 26 | empty |
| 4 | 78 | 0.31 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2206 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 1KKR · Crystal structure of citrobacter amalonaticus methylaspartate ammonia lyase containing… · the same entry in another collection · chain A against A, TM-score 1.00
- O66145 · AlphaFold monomer V2.0 prediction for methylaspartate ammonia-lyase (O66145) · 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 O66145
- Elsewhere: RCSB PDB 1KKR · PDBe 1KKR · UniProt O66145
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