MolNFT v1 · #113752 · protein

Structural basis of neurohormone perception by the receptor tyrosine kinase torso

5AOQ: “Structural basis of neurohormone perception by the receptor tyrosine kinase torso”. X-ray diffraction, 1 ligand (NAG), 10 pockets (best druggability 0.86). MolNFT v1 #113752 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5AOQ
Type: protein
Length: 640 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Torso; Preproptth
EC: 2.7.10.1
UniProt: D2IYS2, Q17238
Ligands: NAG
Pockets: 10 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Torso (EC 2.7.10.1)	protein	233	10% helix, 44% strand	D2IYS2
L	Preproptth	protein	86	0% helix, 41% strand	Q17238
M	Preproptth	protein	88	3% helix, 38% strand	Q17238

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1103	0.86	0.86	115	empty
2	55	0.67	0.96	16	empty
3	241	0.55	0.78	31	empty
4	215	0.54	0.78	32	empty
5	167	0.52	0.79	34	empty

Interfaces

6 interfaces between chains.

L–M · 1361 Å² buried · 12 hydrogen bonds · protein-protein
B–L · 934 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 880 Å² buried · 10 hydrogen bonds · protein-protein
A–M · 774 Å² buried · 6 hydrogen bonds · protein-protein
B–M · 593 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 15 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

5AOQ · Structural basis of neurohormone perception by the receptor tyrosine kinase Torso · the same entry in another collection · chain A against A, TM-score 1.00
D2IYS2 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase receptor torso (D2IYS2) · a predicted model of the same protein · chain A against A, TM-score 0.88

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 D2IYS2
Every structure of UniProt Q17238
Elsewhere: RCSB PDB 5AOQ · PDBe 5AOQ · UniProt D2IYS2 · UniProt Q17238

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