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Crystal structure of threonine aldolase (low-specificity)
Analyse Crystal structure of threonine aldolase (low-specificity) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JG8
- Type
- protein
- Length
- 1,370 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-allo-threonine aldolase
- EC
- 4.1.2.5
- UniProt
- Q9X266
- Ligands
- CA, NA
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-allo-threonine aldolase (EC 4.1.2.5) | protein | 343 | 47% helix, 18% strand | Q9X266 |
| C | L-allo-threonine aldolase (EC 4.1.2.5) | protein | 340 | 46% helix, 18% strand | Q9X266 |
| D | L-allo-threonine aldolase (EC 4.1.2.5) | protein | 344 | 47% helix, 18% strand | Q9X266 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, D, B, C
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.69 | 0.98 | 19 | empty |
| 2 | 482 | 0.69 | 0.80 | 55 | NA |
| 3 | 547 | 0.66 | 0.77 | 52 | empty |
| 4 | 351 | 0.64 | 0.80 | 36 | empty |
| 5 | 324 | 0.64 | 0.80 | 43 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1955 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1895 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1011 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 991 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 828 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 1JG8 · Crystal Structure of Threonine Aldolase (Low-specificity) · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9X266
- Elsewhere: RCSB PDB 1JG8 · PDBe 1JG8 · UniProt Q9X266
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