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Crystal structure of sulfate-bound human l-asparaginase protein
Analyse Crystal structure of sulfate-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
- 4PVQ
- Type
- protein
- Length
- 590 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.13
- Source
- Homo sapiens
- Molecule
- Isoaspartyl peptidase/L-asparaginase
- EC
- 3.4.19.5, 3.5.1.1
- UniProt
- Q7L266
- Ligands
- NA, SO4, IOD
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · resolution 2.13 · 2 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoaspartyl peptidase/L-asparaginase (EC 3.4.19.5, 3.5.1.1) | protein | 294 | 35% helix, 27% strand | Q7L266 |
| B | Isoaspartyl peptidase/L-asparaginase (EC 3.4.19.5, 3.5.1.1) | protein | 296 | 35% helix, 26% strand | Q7L266 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 13 copies · chains A, B
- IOD · Iodide ion · ion · 4 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.57 | 0.82 | 25 | empty |
| 2 | 127 | 0.47 | 0.79 | 29 | SO4 |
| 3 | 87 | 0.40 | 0.78 | 27 | SO4 |
| 4 | 57 | 0.28 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1874 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 4PVQ · Crystal structure of sulfate-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 4PVQ · PDBe 4PVQ · UniProt Q7L266
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