MolNFT v1 · #103914 · protein
Crystal structure of potassium-dependent plant-type L-asparaginase from phaseolus vulgaris in complex with K+ and na+ cations
4PV2 · L-asparaginase alpha subunit: “Crystal structure of potassium-dependent plant-type L-asparaginase from phaseolus vulgaris in complex with K+…”. X-ray diffraction, 3 ligands (NA, K, NO3), 4 pockets (best druggability 0.64). MolNFT v1…
- PDB
- 4PV2
- Type
- protein
- Length
- 575 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, K, NO3
- Pockets
- 4 · best druggability 0.64
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 | 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
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