Research workbench
Crystal structure of linker less pyrococcus furiosus L-asparaginase
Analyse Crystal structure of linker less pyrococcus furiosus L-asparaginase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RA6
- Type
- protein
- Length
- 607 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase
- EC
- 3.5.1.1
- UniProt
- Q8TZE8
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase (EC 3.5.1.1) | protein | 177 | 29% helix, 23% strand | Q8TZE8 |
| B | L-asparaginase (EC 3.5.1.1) | protein | 125 | 34% helix, 16% strand | Q8TZE8 |
| P | L-asparaginase (EC 3.5.1.1) | protein | 178 | 31% helix, 25% strand | Q8TZE8 |
| Q | L-asparaginase (EC 3.5.1.1) | protein | 127 | 34% helix, 15% strand | Q8TZE8 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.51 | 0.79 | 26 | empty |
| 2 | 126 | 0.44 | 0.77 | 24 | empty |
| 3 | 72 | 0.37 | 0.78 | 17 | empty |
| 4 | 63 | 0.30 | 0.74 | 17 | empty |
| 5 | 53 | 0.26 | 0.73 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–B · 939 Ų buried · 10 hydrogen bonds · protein-protein
- P–Q · 931 Ų buried · 12 hydrogen bonds · protein-protein
- B–Q · 901 Ų buried · 9 hydrogen bonds · protein-protein
- A–Q · 856 Ų buried · 13 hydrogen bonds · protein-protein
- B–P · 799 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
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 Q8TZE8
- Elsewhere: RCSB PDB 4RA6 · PDBe 4RA6 · UniProt Q8TZE8
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