Research workbench
Asparaginase II from escherichia COLI
Analyse Asparaginase II from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UOG
- Type
- protein
- Length
- 2,608 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase 2
- EC
- 3.5.1.1
- UniProt
- A0A376KNM9
- Ligands
- ASP
- Pockets
- 19 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | L-asparaginase 2 (EC 3.5.1.1) | protein | 326 | 33% helix, 23% strand | A0A376KNM9 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 8 copies · chains A, C, B, D, E, G, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.89 | 0.91 | 219 | ASP |
| 2 | 1067 | 0.89 | 0.91 | 200 | empty |
| 3 | 279 | 0.81 | 0.93 | 61 | empty |
| 4 | 235 | 0.79 | 0.93 | 57 | empty |
| 5 | 145 | 0.78 | 0.95 | 38 | ASP |
Interfaces
16 interfaces between chains.
- B–D · 2446 Ų buried · 52 hydrogen bonds · protein-protein
- F–H · 2446 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 2445 Ų buried · 54 hydrogen bonds · protein-protein
- E–G · 2437 Ų buried · 50 hydrogen bonds · protein-protein
- G–H · 1119 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6UOG · Asparaginase II from Escherichia coli · the same entry in another collection · chain H against H, 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 A0A376KNM9
- Elsewhere: RCSB PDB 6UOG · PDBe 6UOG · UniProt A0A376KNM9
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