Research workbench
X-ray structure of L-threonine aldolase (low-specificity) in complex with glycine
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
- 1LW5
- 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
- PLG, PLP, CA, CL
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 47% 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 | 47% 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
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · 3 copies · chains B, C, A, D
- 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, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.74 | 0.97 | 24 | empty |
| 2 | 600 | 0.72 | 0.80 | 71 | PLG |
| 3 | 358 | 0.70 | 0.83 | 54 | PLG |
| 4 | 286 | 0.70 | 0.85 | 47 | PLG, PLP |
| 5 | 401 | 0.67 | 0.80 | 51 | CL |
Interfaces
6 interfaces between chains.
- A–D · 1939 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1879 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 965 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 958 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 733 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 modified, 1 cofactor (engineered, cofactor, pyridoxal phosphate Schiff base).
Compared structures
- 1LW5 · X-ray structure of L-Threonine Aldolase (low-specificity) in complex with glycine · the same entry in another collection · chain B against B, 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 1LW5 · PDBe 1LW5 · UniProt Q9X266
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