Research workbench
Complex of mutant (K173M) of pseudomonas 7A glutaminase-asparaginase with L-glu at pH 5. covalent acyl-enzyme intermediate
Analyse Complex of mutant (K173M) of pseudomonas 7A glutaminase-asparaginase with L-glu… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WZ6
- 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
- GLU
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutaminase-asparaginase (EC 3.5.1.38) | protein | 330 | 32% helix, 23% strand | Q88K39 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, 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 | 1153 | 0.88 | 0.90 | 141 | empty |
| 2 | 110 | 0.54 | 0.84 | 33 | GLU |
| 3 | 111 | 0.43 | 0.78 | 26 | empty |
| 4 | 67 | 0.39 | 0.80 | 23 | GLU |
| 5 | 50 | 0.38 | 0.81 | 18 | GLU |
Interfaces
6 interfaces between chains.
- A–B · 2523 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 2496 Ų buried · 50 hydrogen bonds · protein-protein
- B–D · 1277 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1271 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1132 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6WZ6 · Complex of mutant (K173M) of Pseudomonas 7A Glutaminase-Asparaginase with L-Glu at pH 5.… · 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 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 Q88K39
- Elsewhere: RCSB PDB 6WZ6 · PDBe 6WZ6 · UniProt Q88K39
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