Research workbench

Structure of the ectodomain of the human type 1 insulin-like growth factor receptor

Analyse Structure of the ectodomain of the human type 1 insulin-like growth factor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5U8R
Type: protein
Length: 1,027 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Insulin-like growth factor 1 receptor; Fv 24-60 heavy chain; Fv 24-60 light chain
EC: 2.7.10.1
UniProt: P08069
Ligands: MLT, NAG, SO4
Pockets: 12 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Insulin-like growth factor 1 receptor (EC 2.7.10.1)	protein	801	8% helix, 35% strand	P08069
H	Fv 24-60 heavy chain	protein	118	3% helix, 48% strand	—
L	Fv 24-60 light chain	protein	108	3% helix, 48% strand	—

Ligands and binding sites

MLT · D-malate · ligand · 2 copies · chains A, H
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, H
SO4 · Sulfate ion · ion · chains A
IMD · Imidazole · additive · chains H, L

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

Pockets

12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	710	0.68	0.76	49	empty
2	446	0.59	0.75	52	empty
3	122	0.44	0.77	19	empty
4	127	0.41	0.75	22	empty
5	74	0.41	0.79	18	empty

Interfaces

3 interfaces between chains.

H–L · 857 Å² buried · 15 hydrogen bonds · protein-protein
A–H · 846 Å² buried · 15 hydrogen bonds · protein-protein
A–L · 255 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 19 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

5U8R · Structure of the ectodomain of the human Type 1 insulin-like growth factor receptor · 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 P08069
Elsewhere: RCSB PDB 5U8R · PDBe 5U8R · UniProt P08069

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.