Research workbench
Crystal structure of pseudomonas 7A glutaminase-asparaginase (mutant K173M) in complex with D-glu at pH 5.5
Analyse Crystal structure of pseudomonas 7A glutaminase-asparaginase (mutant K173M) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WYZ
- Type
- protein
- Length
- 1,253 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
- DGL
- Pockets
- 10 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Glutaminase-asparaginase (EC 3.5.1.38) | protein | 312 | 34% helix, 21% strand | Q88K39 |
| B | Glutaminase-asparaginase (EC 3.5.1.38) | protein | 315 | 34% helix, 24% strand | Q88K39 |
| C | Glutaminase-asparaginase (EC 3.5.1.38) | protein | 314 | 34% helix, 24% strand | Q88K39 |
Ligands and binding sites
- DGL · D-glutamic 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
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.88 | 0.89 | 136 | empty |
| 2 | 274 | 0.62 | 0.80 | 31 | DGL |
| 3 | 258 | 0.61 | 0.80 | 26 | empty |
| 4 | 308 | 0.61 | 0.78 | 31 | DGL |
| 5 | 276 | 0.60 | 0.79 | 32 | DGL |
Interfaces
6 interfaces between chains.
- A–B · 2323 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 2294 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 1133 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1128 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 909 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6WYZ · Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase (mutant K173M) in complex… · 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 6WYZ · PDBe 6WYZ · UniProt Q88K39
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