Research workbench
Erwinia chrysanthemi L-asparaginase E63Q +S254N mutation + L-aspartic acid
Analyse Erwinia chrysanthemi L-asparaginase E63Q +S254N mutation + L-aspartic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I4B
- Type
- protein
- Length
- 975 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase
- EC
- 3.5.1.1
- UniProt
- P06608
- Ligands
- ASP
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | L-asparaginase (EC 3.5.1.1) | protein | 325 | 32% helix, 22% strand | P06608 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.69 | 0.95 | 29 | empty |
| 2 | 581 | 0.68 | 0.78 | 59 | empty |
| 3 | 265 | 0.65 | 0.82 | 42 | ASP |
| 4 | 255 | 0.65 | 0.82 | 42 | ASP |
| 5 | 53 | 0.53 | 0.89 | 22 | empty |
Interfaces
2 interfaces between chains.
- B–C · 2441 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 316 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5I4B · Erwinia chrysanthemi L-asparaginase E63Q +S254N mutation + L-Aspartic acid · the same entry in another collection · chain C against C, TM-score 1.00
- P06608 · AlphaFold monomer V2.0 prediction for L-asparaginase (P06608) · a predicted model of the same protein · chain C 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 P06608
- Elsewhere: RCSB PDB 5I4B · PDBe 5I4B · UniProt P06608
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