Research workbench
Crystal structure of truncated pyrococcus furiosus L-asparaginase with peptide
Analyse Crystal structure of truncated pyrococcus furiosus L-asparaginase with peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B5U
- Type
- protein
- Length
- 310 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase; Leu-val-val-asn
- EC
- 3.5.1.1
- UniProt
- Q8TZE8
- Ligands
- ASP, CL
- Pockets
- 3 · best druggability 0.39
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase (EC 3.5.1.1) | protein | 175 | 31% helix, 26% strand | Q8TZE8 |
| B | L-asparaginase (EC 3.5.1.1) | protein | 127 | 35% helix, 14% strand | Q8TZE8 |
| C, E | Leu-val-val-asn | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- ASP · Aspartic acid · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A
- IPA · Isopropyl alcohol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.39 | 0.80 | 25 | empty |
| 2 | 79 | 0.33 | 0.74 | 18 | empty |
| 3 | 51 | 0.33 | 0.79 | 19 | ASP, GOL |
Interfaces
3 interfaces between chains.
- A–B · 917 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 252 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 235 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5B5U · Crystal structure of truncated Pyrococcus furiosus L-asparaginase with peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q8TZE8 · AlphaFold monomer V2.0 prediction for L-asparaginase (Q8TZE8) · 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 Q8TZE8
- Elsewhere: RCSB PDB 5B5U · PDBe 5B5U · UniProt Q8TZE8
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