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X-ray structure of L-threonine aldolase (low-specificity) in complex with L-allo-threonine
Analyse X-ray structure of L-threonine aldolase (low-specificity) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LW4
- Type
- protein
- Length
- 1,373 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
- TLP, PLP, CA, CL
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | L-allo-threonine aldolase (EC 4.1.2.5) | protein | 343 | 46% helix, 18% strand | Q9X266 |
| D | L-allo-threonine aldolase (EC 4.1.2.5) | protein | 344 | 46% helix, 17% strand | Q9X266 |
Ligands and binding sites
- TLP · 3-hydroxy-2-[(3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl)-amino]-butyric acid · ligand · 3 copies · chains B, C, D, A
- PLP · Pyridoxal-5'-phosphate · ligand · chains B, C
- CA · Calcium ion · metal · 6 copies · chains A, D, B, C
- CL · Chloride ion · ion · 6 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.74 | 0.97 | 25 | empty |
| 2 | 629 | 0.73 | 0.80 | 79 | TLP |
| 3 | 370 | 0.71 | 0.83 | 54 | TLP |
| 4 | 379 | 0.71 | 0.83 | 55 | TLP, PLP |
| 5 | 497 | 0.69 | 0.80 | 59 | CL |
Interfaces
6 interfaces between chains.
- A–D · 1914 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1881 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 962 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 955 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 773 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 modified, 1 cofactor (engineered, cofactor, pyridoxal phosphate Schiff base).
Compared structures
- 1LW4 · X-ray structure of L-Threonine Aldolase (low-specificity) in complex with L-allo-threonine · the same entry in another collection · chain C against C, 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 1LW4 · PDBe 1LW4 · UniProt Q9X266
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