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Insulin receptor ectodomain construct comprising domains L1,CR,L2, fniii-1 and alphact peptide in complex with bovine insulin and Fab 83-14 (revised structure)

Analyse Insulin receptor ectodomain construct comprising domains L1,CR,L2, fniii-1 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KQV
Type: protein
Length: 2,120 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Insulin; Monoclonal antibody Fab 83-14 - heavy chain; Monoclonal antibody Fab 83-14…
EC: 2.7.10.1
UniProt: P01317, P06213
Ligands: NAG, FUC
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 7 distinct chains · 10% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, I	Insulin	protein	21	43% helix, 0% strand	P01317
B, J	Insulin	protein	17	71% helix, 0% strand	P01317
C	Monoclonal antibody Fab 83-14 - heavy chain	protein	211	6% helix, 52% strand	—
D, Q	Monoclonal antibody Fab 83-14 - light chain	protein	214	6% helix, 50% strand	—
E	Insulin RECEPTOR,INSULIN receptor (EC 2.7.10.1)	protein	593	10% helix, 31% strand	P06213
F	Insulin RECEPTOR,INSULIN receptor (EC 2.7.10.1)	protein	592	10% helix, 31% strand	P06213
P	Monoclonal antibody Fab 83-14 - heavy chain	protein	220	5% helix, 50% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains E, F
FUC · alpha-L-fucopyranose · sugar · 3 copies · chains F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1177	0.86	0.87	93	empty
2	287	0.58	0.77	38	empty
3	71	0.58	0.89	22	empty
4	200	0.58	0.80	26	empty
5	252	0.56	0.77	32	empty

Interfaces

13 interfaces between chains.

C–D · 1857 Å² buried · 11 hydrogen bonds · protein-protein
P–Q · 1848 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 1398 Å² buried · 18 hydrogen bonds · protein-protein
F–P · 573 Å² buried · 11 hydrogen bonds · protein-protein
C–E · 561 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 49 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

5KQV · Insulin receptor ectodomain construct comprising domains L1,CR,L2, FnIII-1 and alphaCT… · the same entry in another collection · chain Q against Q, TM-score 1.00
P06213 · AlphaFold monomer V2.0 prediction for insulin receptor (P06213) · a predicted model of the same protein · chain F against A, TM-score 0.60

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 P01317
Every structure of UniProt P06213
Elsewhere: RCSB PDB 5KQV · PDBe 5KQV · UniProt P01317 · UniProt P06213

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