Research workbench
Crystal structure of the gsuk bound to ADP
Analyse Crystal structure of the gsuk bound to ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GX1
- Type
- protein
- Length
- 1,845 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trka domain protein
- UniProt
- Q74FS9
- Ligands
- ADP, GLC, K, ZN, CA, PO4
- Pockets
- 18 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trka domain protein | protein | 376 | 53% helix, 14% strand | Q74FS9 |
| B | Trka domain protein | protein | 547 | 43% helix, 19% strand | Q74FS9 |
| C | Trka domain protein | protein | 546 | 44% helix, 19% strand | Q74FS9 |
| D | Trka domain protein | protein | 376 | 55% helix, 14% strand | Q74FS9 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains B, C, D
- K · Potassium ion · metal · 11 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 · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.75 | 0.78 | 121 | ADP |
| 2 | 1089 | 0.73 | 0.76 | 65 | PO4 |
| 3 | 970 | 0.72 | 0.76 | 68 | PO4 |
| 4 | 499 | 0.69 | 0.80 | 63 | ADP |
| 5 | 445 | 0.63 | 0.77 | 64 | ADP |
Interfaces
2 interfaces between chains.
- A–B · 1817 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1644 Ų buried · 10 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 4GX1 · PDBe 4GX1 · UniProt Q74FS9
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