Research workbench
Crystal structure of the trka gating ring bound to ATP-gamma-S
Analyse Crystal structure of the trka gating ring bound to ATP-gamma-S in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J9V
- Type
- protein
- Length
- 910 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Potassium uptake protein trka
- UniProt
- Q87KD2
- Ligands
- AGS, MG, SO4
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium uptake protein trka | protein | 456 | 32% helix, 25% strand | Q87KD2 |
| B | Potassium uptake protein trka | protein | 454 | 35% helix, 26% strand | Q87KD2 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.76 | 0.84 | 61 | empty |
| 2 | 314 | 0.64 | 0.80 | 40 | empty |
| 3 | 107 | 0.58 | 0.85 | 19 | empty |
| 4 | 89 | 0.49 | 0.82 | 21 | empty |
| 5 | 176 | 0.48 | 0.77 | 30 | AGS |
Interfaces
1 interface between chains.
- A–B · 826 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4J9V · Crystal Structure of the TrkA Gating ring bound to ATP-gamma-S · the same entry in another collection · 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 Q87KD2
- Elsewhere: RCSB PDB 4J9V · PDBe 4J9V · UniProt Q87KD2
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