MolNFT v1 · #103939 · protein
Crystal structure of partially-cleaved human L-asparaginase protein in complex with L-aspartate
4PVR · Isoaspartyl PEPTIDASE/L-asparaginase: “Crystal structure of partially-cleaved human L-asparaginase protein in complex with L-aspartate”. X-ray diffraction, 2 ligands (ASP, NA), 2 pockets (best druggability 0.58). MolNFT v1 #103939…
- PDB
- 4PVR
- 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
- ASP, NA
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 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 | 298 | 35% helix, 26% strand | Q7L266 |
| B | Isoaspartyl PEPTIDASE/L-asparaginase (EC 3.4.19.5, 3.5.1.1) | protein | 295 | 36% helix, 26% strand | Q7L266 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.58 | 0.79 | 32 | ASP |
| 2 | 112 | 0.43 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1872 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 4PVR · Crystal structure of partially-cleaved human l-asparaginase protein in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- Q7L266 · AlphaFold monomer V2.0 prediction for isoaspartyl PEPTIDASE/L-asparaginase (Q7L266) · a predicted model of the same protein · chain B 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 4PVR · PDBe 4PVR · UniProt Q7L266
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