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Crystal structure of L-threonine aldolase from pseudomonas putida
Analyse Crystal structure of L-threonine aldolase from pseudomonas putida in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VYE
- Type
- protein
- Length
- 1,371 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-threonine aldolase
- EC
- 4.1.2.48
- UniProt
- A0A166JNM8
- Ligands
- PLR
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-threonine aldolase (EC 4.1.2.48) | protein | 343 | 44% helix, 17% strand | A0A166JNM8 |
| B | L-threonine aldolase (EC 4.1.2.48) | protein | 344 | 44% helix, 16% strand | A0A166JNM8 |
| C, D | L-threonine aldolase (EC 4.1.2.48) | protein | 342 | 43% helix, 17% strand | A0A166JNM8 |
Ligands and binding sites
- PLR · (5-hydroxy-4,6-dimethylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, C, B, 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 | 561 | 0.77 | 0.84 | 78 | PLR |
| 2 | 477 | 0.74 | 0.83 | 59 | PLR |
| 3 | 401 | 0.73 | 0.84 | 60 | PLR |
| 4 | 390 | 0.73 | 0.84 | 47 | PLR |
| 5 | 93 | 0.70 | 0.94 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2212 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2119 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1109 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1108 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 964 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5VYE · Crystal Structure of L-Threonine Aldolase from Pseudomonas putida · 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 A0A166JNM8
- Elsewhere: RCSB PDB 5VYE · PDBe 5VYE · UniProt A0A166JNM8
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