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Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase in complex with L-Glu at pH 6.5
Analyse Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WYY
- Type
- protein
- Length
- 1,288 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.35
- Source
- Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)
- Molecule
- Glutaminase-asparaginase
- EC
- 3.5.1.38
- UniProt
- Q88K39
- Ligands
- GLU
- Pockets
- 11 · best druggability 0.88
Structure
x-ray diffraction · resolution 1.35 · 3 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutaminase-asparaginase (EC 3.5.1.38) | protein | 315 | 34% helix, 23% strand | Q88K39 |
| B | Glutaminase-asparaginase (EC 3.5.1.38) | protein | 313 | 33% helix, 23% strand | Q88K39 |
| C, D | Glutaminase-asparaginase (EC 3.5.1.38) | protein | 330 | 32% helix, 22% strand | Q88K39 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, D, B, C
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1192 | 0.88 | 0.90 | 138 | empty |
| 2 | 117 | 0.66 | 0.89 | 36 | GLU |
| 3 | 310 | 0.65 | 0.81 | 35 | GLU |
| 4 | 120 | 0.63 | 0.87 | 27 | GLU, EDO |
| 5 | 324 | 0.62 | 0.79 | 32 | GLU |
Interfaces
6 interfaces between chains.
- C–D · 2500 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2301 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 1129 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1124 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1082 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6WYY · Crystal structure of pseudomonas 7A glutaminase-asparaginase in complex with L-glu at pH… · 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 D 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 6WYY · PDBe 6WYY · UniProt Q88K39
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