Research workbench
Crystal structure of human L-asparaginase protein with covalently linked substrate L-asparagine
Analyse Crystal structure of human L-asparaginase protein with covalently linked… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O0H
- Type
- protein
- Length
- 590 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoaspartyl PEPTIDASE/L-asparaginase
- EC
- 3.4.19.5, 3.5.1.1
- UniProt
- Q7L266
- Ligands
- IAS, NA
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isoaspartyl PEPTIDASE/L-asparaginase (EC 3.4.19.5, 3.5.1.1) | protein | 295 | 36% helix, 26% strand | Q7L266 |
Ligands and binding sites
- IAS · Beta-L-aspartic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.63 | 0.81 | 41 | IAS |
| 2 | 272 | 0.61 | 0.80 | 41 | IAS |
| 3 | 98 | 0.38 | 0.75 | 22 | empty |
| 4 | 50 | 0.32 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1882 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4O0H · Crystal structure of human L-asparaginase protein with covalently linked substrate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7L266 · AlphaFold monomer V2.0 prediction for isoaspartyl PEPTIDASE/L-asparaginase (Q7L266) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q7L266
- Elsewhere: RCSB PDB 4O0H · PDBe 4O0H · UniProt Q7L266
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