Research workbench
Crystal structure of potassium-dependent plant-type L-asparaginase from phaseolus vulgaris in complex with 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
- 4PV3
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase alpha subunit; L-asparaginase beta subunit
- EC
- 3.5.1.1
- UniProt
- V7CU13
- Ligands
- NA
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 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 | 157 | 49% helix, 18% strand | V7CU13 |
| B, D | L-asparaginase beta subunit (EC 3.5.1.1) | protein | 131 | 23% helix, 37% strand | V7CU13 |
| C | L-asparaginase alpha subunit (EC 3.5.1.1) | protein | 155 | 46% helix, 18% strand | V7CU13 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, 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 | 465 | 0.65 | 0.78 | 49 | empty |
| 2 | 407 | 0.62 | 0.77 | 45 | empty |
| 3 | 107 | 0.43 | 0.78 | 22 | empty |
| 4 | 78 | 0.34 | 0.76 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2842 Ų buried · 56 hydrogen bonds · protein-protein
- C–D · 2836 Ų buried · 55 hydrogen bonds · protein-protein
- B–D · 625 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 606 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 595 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4PV3 · 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 4PV3 · PDBe 4PV3 · UniProt V7CU13
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.