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Insulin receptor ectodomain dimer complexed with two irpa-3 partial agonists

Analyse Insulin receptor ectodomain dimer complexed with two irpa-3 partial agonists in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MD4
Type: protein
Length: 1,720 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isoform short of insulin receptor subunit alpha; Isoform short of insulin receptor…
UniProt: P06213, P01308
Pockets: 18 · best druggability 0.77

Structure

electron microscopy · 8 distinct chains · 12% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
N	Isoform short of insulin receptor subunit alpha	protein	22	86% helix, 0% strand	P06213
M	Isoform short of insulin receptor subunit alpha	protein	11	73% helix, 0% strand	P06213
B	Isoform short of insulin receptor	protein	778	8% helix, 30% strand	P06213
A	Isoform short of insulin receptor	protein	724	8% helix, 31% strand	P06213
U, S, Q, O	Insulin chain a	protein	21	52% helix, 0% strand	P01308
V	Insulin B chain	protein	28	57% helix, 0% strand	P01308
T	Insulin B chain	protein	27	56% helix, 4% strand	P01308
R, P	Insulin B chain	protein	23	48% helix, 0% strand	P01308

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	107	0.77	0.96	35	empty
2	107	0.76	0.96	36	empty
3	863	0.75	0.79	63	empty
4	69	0.71	0.96	26	empty
5	610	0.64	0.75	66	empty

Interfaces

23 interfaces between chains.

B–A · 1055 Å² buried · 9 hydrogen bonds · protein-protein
U–V · 552 Å² buried · 4 hydrogen bonds · protein-protein
S–T · 541 Å² buried · 4 hydrogen bonds · protein-protein
O–P · 529 Å² buried · 9 hydrogen bonds · protein-protein
Q–R · 522 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 38 disulfide (disulfide).

Compared structures

7MD4 · Insulin receptor ectodomain dimer complexed with two IRPA-3 partial agonists · the same entry in another collection · chain N against N, 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 P06213
Every structure of UniProt P01308
Elsewhere: RCSB PDB 7MD4 · PDBe 7MD4 · UniProt P06213 · UniProt P01308

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