MolNFT v1 · #166902 · protein
Structure of trkh-trka in complex with atpgammas
6V4L · Trk system potassium uptake protein trkh: “Structure of trkh-trka in complex with atpgammas”. X-ray diffraction, 1 ligand (AGS), 20 pockets (best druggability 0.82). MolNFT v1 #166902 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6V4L
- Type
- protein
- Length
- 1,855 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trk system potassium uptake protein trkh; Potassium uptake protein trka
- UniProt
- Q87TN7, Q87KD2
- Ligands
- AGS
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Trk system potassium uptake protein trkh | protein | 479 | 61% helix, 0% strand | Q87TN7 |
| C | Potassium uptake protein trka | protein | 449 | 30% helix, 21% strand | Q87KD2 |
| D | Potassium uptake protein trka | protein | 448 | 32% helix, 22% strand | Q87KD2 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.82 | 0.83 | 63 | empty |
| 2 | 265 | 0.68 | 0.84 | 48 | empty |
| 3 | 436 | 0.67 | 0.79 | 51 | empty |
| 4 | 298 | 0.64 | 0.81 | 32 | empty |
| 5 | 255 | 0.63 | 0.81 | 33 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2216 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 152 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 110 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 28 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 26 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6V4L · Structure of TrkH-TrkA in complex with ATPgammaS · the same entry in another collection · chain A against A, TM-score 1.00
- Q87TN7 · AlphaFold monomer V2.0 prediction for trk system potassium uptake protein trkh (Q87TN7) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q87TN7
- Every structure of UniProt Q87KD2
- Elsewhere: RCSB PDB 6V4L · PDBe 6V4L · UniProt Q87TN7 · UniProt Q87KD2
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