MolNFT v1 · #135762 · protein
Structure of the ectodomain of the human type 1 insulin-like growth factor receptor in complex with igf-I
5U8Q · Insulin-like growth factor 1 receptor: “Structure of the ectodomain of the human type 1 insulin-like growth factor receptor in complex with igf-I”. X-ray diffraction, 4 ligands (MLT, NAG, MAN), 10 pockets (best druggability 0.69).…
- PDB
- 5U8Q
- Type
- protein
- Length
- 1,074 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-like growth factor 1 receptor; Insulin-like growth factor I; Fv 24-60 heavy…
- EC
- 2.7.10.1
- UniProt
- P08069, P05019
- Ligands
- MLT, NAG, MAN, SO4
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 36% 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, 34% strand | P08069 |
| B | Insulin-like growth factor I | protein | 48 | 44% helix, 4% strand | P05019 |
| H | Fv 24-60 heavy chain | protein | 118 | 8% helix, 47% strand | — |
| L | Fv 24-60 light chain | protein | 107 | 3% helix, 51% strand | — |
Ligands and binding sites
- MLT · D-malate · ligand · chains A, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, H
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.69 | 0.78 | 66 | empty |
| 2 | 652 | 0.66 | 0.76 | 54 | empty |
| 3 | 151 | 0.50 | 0.79 | 21 | empty |
| 4 | 89 | 0.45 | 0.80 | 19 | empty |
| 5 | 133 | 0.41 | 0.75 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1051 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 885 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 872 Ų buried · 15 hydrogen bonds · protein-protein
- A–L · 190 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5U8Q · Structure of the ectodomain of the human Type 1 insulin-like growth factor receptor in… · the same entry in another collection · chain A against A, TM-score 1.00
- P05019 · AlphaFold monomer V2.0 prediction for insulin-like growth factor I (P05019) · a predicted model of the same protein · chain B against A, TM-score 0.75
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
- Every structure of UniProt P05019
- Elsewhere: RCSB PDB 5U8Q · PDBe 5U8Q · UniProt P08069 · UniProt P05019
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