Research workbench
Wolinella succinogenes L-asparaginase P121 and L-aspartic acid
Analyse Wolinella succinogenes L-asparaginase P121 and L-aspartic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K3O
- Type
- protein
- Length
- 1,312 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase
- EC
- 3.5.1.1
- UniProt
- P50286
- Ligands
- ASP
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-asparaginase (EC 3.5.1.1) | protein | 328 | 33% helix, 23% strand | P50286 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.72 | 0.77 | 73 | empty |
| 2 | 91 | 0.64 | 0.90 | 32 | empty |
| 3 | 97 | 0.59 | 0.87 | 27 | empty |
| 4 | 112 | 0.49 | 0.81 | 27 | empty |
| 5 | 104 | 0.48 | 0.81 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2363 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 2357 Ų buried · 51 hydrogen bonds · protein-protein
- B–C · 243 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 P50286
- Elsewhere: RCSB PDB 5K3O · PDBe 5K3O · UniProt P50286
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