Research workbench
Crystal structure of the asp-bound guinea pig L-asparaginase 1 catalytic domain
Analyse Crystal structure of the asp-bound guinea pig L-asparaginase 1 catalytic domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R8L
- Type
- protein
- Length
- 1,418 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- EC
- 3.5.1.1
- UniProt
- H0W0T5
- Ligands
- ASP
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Uncharacterized protein (EC 3.5.1.1) | protein | 354 | 28% helix, 25% strand | H0W0T5 |
| B, D | Uncharacterized protein (EC 3.5.1.1) | protein | 355 | 28% helix, 25% strand | H0W0T5 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.85 | 0.94 | 69 | empty |
| 2 | 505 | 0.85 | 0.91 | 92 | empty |
| 3 | 316 | 0.72 | 0.85 | 31 | empty |
| 4 | 634 | 0.72 | 0.79 | 67 | empty |
| 5 | 235 | 0.59 | 0.80 | 35 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2052 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 2041 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1204 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1145 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4R8L · Crystal structure of the Asp-bound guinea pig L-asparaginase 1 catalytic domain · 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 H0W0T5
- Elsewhere: RCSB PDB 4R8L · PDBe 4R8L · UniProt H0W0T5
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