Research workbench
Crystal structure of the gsuk L97D mutant
Analyse Crystal structure of the gsuk L97D mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GX0
- Type
- protein
- Length
- 1,844 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trka domain protein
- UniProt
- Q74FS9
- Ligands
- GLC, K, ZN, CA, PO4
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trka domain protein | protein | 375 | 52% helix, 14% strand | Q74FS9 |
| B | Trka domain protein | protein | 547 | 46% helix, 19% strand | Q74FS9 |
| C | Trka domain protein | protein | 546 | 44% helix, 19% strand | Q74FS9 |
| D | Trka domain protein | protein | 376 | 52% helix, 13% strand | Q74FS9 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 5 copies · chains A, B, D
- K · Potassium ion · metal · 12 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.73 | 0.76 | 63 | PO4, GLC |
| 2 | 685 | 0.72 | 0.78 | 55 | PO4 |
| 3 | 381 | 0.66 | 0.80 | 47 | empty |
| 4 | 481 | 0.64 | 0.77 | 67 | PO4 |
| 5 | 399 | 0.62 | 0.76 | 37 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1804 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1634 Ų buried · 6 hydrogen bonds · protein-protein
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 Q74FS9
- Elsewhere: RCSB PDB 4GX0 · PDBe 4GX0 · UniProt Q74FS9
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