Research workbench
Crystal structure of malonate-bound human L-asparaginase protein
Analyse Crystal structure of malonate-bound human L-asparaginase protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PVP
- Type
- protein
- Length
- 593 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
- NA
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoaspartyl PEPTIDASE/L-asparaginase (EC 3.4.19.5, 3.5.1.1) | protein | 297 | 35% helix, 26% strand | Q7L266 |
| B | Isoaspartyl PEPTIDASE/L-asparaginase (EC 3.4.19.5, 3.5.1.1) | protein | 296 | 35% helix, 25% strand | Q7L266 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.61 | 0.79 | 38 | empty |
| 2 | 57 | 0.46 | 0.85 | 19 | empty |
| 3 | 130 | 0.42 | 0.76 | 30 | MLI |
Interfaces
1 interface between chains.
- A–B · 1910 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4PVP · Crystal structure of malonate-bound human L-asparaginase protein · 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 4PVP · PDBe 4PVP · UniProt Q7L266
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