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Crystal structure of the TRKH/TRKA potassium transport complex

Analyse Crystal structure of the TRKH/TRKA potassium transport complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4J9U
Type: protein
Length: 3,645 residues
Chains: 8
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: TBR, NAD, K
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 5 distinct chains · 38% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Trk system potassium uptake protein trkh	protein	462	60% helix, 1% strand	Q87TN7
E	Potassium uptake protein trka	protein	451	33% helix, 24% strand	Q87KD2
F	Potassium uptake protein trka	protein	444	32% helix, 25% strand	Q87KD2
G	Potassium uptake protein trka	protein	452	31% helix, 24% strand	Q87KD2
H	Potassium uptake protein trka	protein	450	32% helix, 24% strand	Q87KD2

Ligands and binding sites

TBR · Hexatantalum dodecabromide · ligand · 18 copies · chains A, E, F, B, G, H, C, D
NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains E, F, G, H
K · Potassium ion · metal · 4 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1113	0.80	0.81	108	empty
2	1190	0.80	0.81	79	empty
3	1187	0.80	0.81	78	empty
4	709	0.79	0.83	64	TBR
5	940	0.77	0.80	96	NAD, TBR

Interfaces

22 interfaces between chains.

C–D · 2200 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 2186 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 972 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 944 Å² buried · 7 hydrogen bonds · protein-protein
F–G · 877 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4J9U · Crystal Structure of the TrkH/TrkA potassium transport complex · the same entry in another collection · chain H against H, 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 0.97

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 4J9U · PDBe 4J9U · UniProt Q87TN7 · UniProt Q87KD2

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