Research workbench
Crystal structure of potassium-dependent plant-type L-asparaginase from Phaseolus vulgaris in complex with K+ and Na+ cations
Analyse Crystal structure of potassium-dependent plant-type L-asparaginase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PV2
- Type
- protein
- Length
- 575 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.79
- Source
- Phaseolus vulgaris
- Molecule
- L-asparaginase alpha subunit; L-asparaginase beta subunit
- EC
- 3.5.1.1
- UniProt
- V7CU13
- Ligands
- NA, K, NO3
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · resolution 1.79 · 3 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase alpha subunit (EC 3.5.1.1) | protein | 155 | 47% helix, 19% strand | V7CU13 |
| B, D | L-asparaginase beta subunit (EC 3.5.1.1) | protein | 131 | 22% helix, 37% strand | V7CU13 |
| C | L-asparaginase alpha subunit (EC 3.5.1.1) | protein | 158 | 48% helix, 18% strand | V7CU13 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, C
- K · Potassium ion · metal · 4 copies · chains A, C, B
- NO3 · Nitrate ion · ion · 21 copies · chains A, B, D, C
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 | 470 | 0.64 | 0.77 | 49 | empty |
| 2 | 377 | 0.62 | 0.78 | 45 | NO3 |
| 3 | 73 | 0.38 | 0.79 | 17 | NO3 |
| 4 | 59 | 0.33 | 0.77 | 19 | K |
Interfaces
6 interfaces between chains.
- C–D · 2813 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 2810 Ų buried · 54 hydrogen bonds · protein-protein
- B–D · 624 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 622 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 596 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4PV2 · Crystal structure of potassium-dependent plant-type L-asparaginase from phaseolus… · 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 V7CU13
- Elsewhere: RCSB PDB 4PV2 · PDBe 4PV2 · UniProt V7CU13
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.