Research workbench
Crystal structure of pseudomonas 7A glutaminase-asparaginase with the inhibitor don covalently bound in the active site
Analyse Crystal structure of pseudomonas 7A glutaminase-asparaginase with the inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DJP
- Type
- protein
- Length
- 660 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaminase-asparaginase
- EC
- 3.5.1.38
- UniProt
- P10182
- Ligands
- DO2
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutaminase-asparaginase (EC 3.5.1.38) | protein | 330 | 32% helix, 21% strand | P10182 |
Ligands and binding sites
- DO2 · 5,5-dihydroxy-6-oxo-L-norleucine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.75 | 0.95 | 38 | empty |
| 2 | 66 | 0.64 | 0.93 | 25 | empty |
| 3 | 81 | 0.42 | 0.79 | 23 | empty |
| 4 | 75 | 0.41 | 0.79 | 18 | empty |
| 5 | 78 | 0.40 | 0.79 | 24 | DO2 |
Interfaces
1 interface between chains.
- A–B · 2518 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1DJP · Crystal structure of pseudomonas 7A glutaminase-asparaginase with the inhibitor don… · the same entry in another collection · chain A against A, TM-score 1.00
- P10182 · AlphaFold monomer V2.0 prediction for glutaminase-asparaginase (P10182) · a predicted model of the same protein · chain A 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 P10182
- Elsewhere: RCSB PDB 1DJP · PDBe 1DJP · UniProt P10182
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