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Structure of TrkH-TrkA in complex with ATP

Analyse Structure of TrkH-TrkA in complex with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6V4J
Type: protein
Length: 2,697 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.97
Source: Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Molecule: Trk system potassium uptake protein TrkH; Potassium uptake protein TrkA
UniProt: Q87TN7, Q87KD2
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 2.97 · 5 distinct chains · 59% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Trk system potassium uptake protein TrkH	protein	447	60% helix, 0% strand	Q87TN7
B	Trk system potassium uptake protein TrkH	protein	434	62% helix, 0% strand	Q87TN7
C	Trk system potassium uptake protein TrkH	protein	442	61% helix, 0% strand	Q87TN7
D	Trk system potassium uptake protein TrkH	protein	438	63% helix, 0% strand	Q87TN7
E, F, G, H	Potassium uptake protein TrkA	protein	234	39% helix, 18% strand	Q87KD2

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	1047	0.89	0.91	168	empty
2	523	0.85	0.91	79	empty
3	513	0.85	0.91	86	empty
4	509	0.85	0.91	89	empty
5	430	0.83	0.90	90	empty

Interfaces

12 interfaces between chains.

C–D · 1417 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 1388 Å² buried · 6 hydrogen bonds · protein-protein
F–H · 624 Å² buried · 24 hydrogen bonds · protein-protein
E–G · 610 Å² buried · 18 hydrogen bonds · protein-protein
B–E · 437 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6V4J · Structure of trkh-trka in complex with ATP · 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 0.89

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 6V4J · PDBe 6V4J · UniProt Q87TN7 · UniProt Q87KD2

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