Research workbench
The thermostable L-asparaginase from thermococcus kodakarensis
Analyse The thermostable L-asparaginase from thermococcus kodakarensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OT0
- Type
- protein
- Length
- 1,968 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase
- UniProt
- Q5JIW4
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | L-asparaginase | protein | 328 | 31% helix, 25% strand | Q5JIW4 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, D, F
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.79 | 0.85 | 82 | PO4 |
| 2 | 110 | 0.78 | 0.98 | 40 | empty |
| 3 | 111 | 0.76 | 0.96 | 50 | EDO |
| 4 | 94 | 0.76 | 0.97 | 39 | empty |
| 5 | 1137 | 0.68 | 0.74 | 89 | empty |
Interfaces
10 interfaces between chains.
- E–F · 2780 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2740 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2703 Ų buried · 42 hydrogen bonds · protein-protein
- A–E · 547 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 330 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5OT0 · The thermostable L-asparaginase from Thermococcus kodakarensis · 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 Q5JIW4
- Elsewhere: RCSB PDB 5OT0 · PDBe 5OT0 · UniProt Q5JIW4
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