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Crystal structure of threonine aldolase
Analyse Crystal structure of threonine aldolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M6S
- 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
- CA, CL
- Pockets
- 9 · best druggability 0.68
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 | 47% helix, 18% strand | Q9X266 |
Ligands and binding sites
- 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
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.68 | 0.81 | 52 | CL |
| 2 | 396 | 0.66 | 0.80 | 47 | CL |
| 3 | 452 | 0.65 | 0.78 | 56 | empty |
| 4 | 306 | 0.64 | 0.80 | 37 | empty |
| 5 | 270 | 0.62 | 0.81 | 31 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1931 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1930 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1008 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 975 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 742 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 1M6S · Crystal Structure Of Threonine Aldolase · 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 1M6S · PDBe 1M6S · UniProt Q9X266
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