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Human insulin in complex with the human insulin microreceptor in turn in complex with fv 83-7

Analyse Human insulin in complex with the human insulin microreceptor in turn in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VEP
Type: protein
Length: 2,371 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Insulin chain a; Insulin B chain; Fv 83-7 heavy chain; Fv 83-7 light chain; Insulin…
EC: 2.7.10.1
UniProt: P01308, P06213
Ligands: NAG, FUC, BMA, MAN
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 16 distinct chains · 10% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G, M, S	Insulin chain a	protein	21	48% helix, 5% strand	P01308
B	Insulin B chain	protein	27	37% helix, 4% strand	P01308
C	Fv 83-7 heavy chain	protein	121	5% helix, 46% strand	—
D	Fv 83-7 light chain	protein	116	3% helix, 48% strand	—
E	Insulin receptor subunit alpha (EC 2.7.10.1)	protein	293	12% helix, 31% strand	P06213
F, L, R, X	Insulin receptor subunit beta (EC 2.7.10.1)	protein	16	56% helix, 0% strand	P06213
H	Insulin B chain	protein	25	40% helix, 4% strand	P01308
I, U	Fv 83-7 heavy chain	protein	117	8% helix, 48% strand	—
J	Fv 83-7 light chain	protein	113	3% helix, 51% strand	—
K	Insulin receptor subunit alpha (EC 2.7.10.1)	protein	294	11% helix, 32% strand	P06213
N, T	Insulin B chain	protein	26	38% helix, 4% strand	P01308
O	Fv 83-7 heavy chain	protein	122	5% helix, 46% strand	—
P	Fv 83-7 light chain	protein	114	3% helix, 51% strand	—
Q	Insulin receptor subunit alpha (EC 2.7.10.1)	protein	302	11% helix, 29% strand	P06213
V	Fv 83-7 light chain	protein	114	3% helix, 49% strand	—
W	Insulin receptor subunit alpha (EC 2.7.10.1)	protein	296	11% helix, 32% strand	P06213

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains E, C, G, K, I, Q, O, W, U, T, M
FUC · alpha-L-fucopyranose · sugar · 9 copies · chains A, B, E, K, Q, W, S, T
BMA · beta-D-mannopyranose · sugar · 8 copies
MAN · alpha-D-mannopyranose · sugar · 2 copies

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

Pockets

20 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	986	0.85	0.86	114	empty
2	957	0.84	0.85	96	empty
3	941	0.75	0.79	82	empty
4	828	0.74	0.78	56	empty
5	783	0.66	0.74	53	empty

Interfaces

52 interfaces between chains.

I–J · 868 Å² buried · 16 hydrogen bonds · protein-protein
O–P · 866 Å² buried · 16 hydrogen bonds · protein-protein
U–V · 866 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 850 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 714 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 76 disulfide, 20 glycan (disulfide, N-glycosylation).

Compared structures

6VEP · Human insulin in complex with the human insulin microreceptor in turn in complex with Fv… · the same entry in another collection · chain J against J, 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 P01308
Every structure of UniProt P06213
Elsewhere: RCSB PDB 6VEP · PDBe 6VEP · UniProt P01308 · UniProt P06213

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