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Crystal structure of monoclinic form of D90E mutant of escherichia COLI asparaginase II
Analyse Crystal structure of monoclinic form of D90E mutant of escherichia COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JAZ
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase II
- EC
- 3.5.1.1
- UniProt
- P00805
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase II (EC 3.5.1.1) | protein | 307 | 33% helix, 21% strand | P00805 |
| B | L-asparaginase II (EC 3.5.1.1) | protein | 305 | 34% helix, 22% strand | P00805 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.40 | 0.77 | 22 | empty |
| 2 | 101 | 0.40 | 0.77 | 21 | empty |
| 3 | 77 | 0.40 | 0.78 | 16 | empty |
| 4 | 83 | 0.39 | 0.78 | 21 | empty |
| 5 | 76 | 0.36 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 763 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1JAZ · Crystal Structure of Monoclinic Form of D90E Mutant of Escherichia coli Asparaginase II · the same entry in another collection · chain A against A, TM-score 1.00
- P00805 · AlphaFold monomer V2.0 prediction for L-asparaginase 2 (P00805) · 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 P00805
- Elsewhere: RCSB PDB 1JAZ · PDBe 1JAZ · UniProt P00805
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