Research workbench
Complex of mutant (K173M) of pseudomonas 7A glutaminase-asparaginase with L-asp at pH 6. covalent acyl-enzyme intermediate
Analyse Complex of mutant (K173M) of pseudomonas 7A glutaminase-asparaginase with L-asp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WZ4
- Type
- protein
- Length
- 1,320 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaminase-asparaginase
- EC
- 3.5.1.38
- UniProt
- Q88K39
- Ligands
- ASP
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutaminase-asparaginase (EC 3.5.1.38) | protein | 330 | 32% helix, 22% strand | Q88K39 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.87 | 0.89 | 100 | empty |
| 2 | 152 | 0.80 | 0.97 | 50 | empty |
| 3 | 100 | 0.37 | 0.74 | 23 | empty |
| 4 | 54 | 0.34 | 0.79 | 20 | ASP |
| 5 | 91 | 0.34 | 0.73 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2522 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2520 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 1263 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1262 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1128 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6WZ4 · Complex of mutant (K173M) of Pseudomonas 7A Glutaminase-Asparaginase with L-Asp at pH 6.… · the same entry in another collection · chain D against D, TM-score 1.00
- Q88K39 · AlphaFold monomer V2.0 prediction for glutaminase-asparaginase (Q88K39) · 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 Q88K39
- Elsewhere: RCSB PDB 6WZ4 · PDBe 6WZ4 · UniProt Q88K39
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