MolNFT v1 · #135763 · protein
Structure of the ectodomain of the human type 1 insulin-like growth factor receptor
5U8R · Insulin-like growth factor 1 receptor: “Structure of the ectodomain of the human type 1 insulin-like growth factor receptor”. X-ray diffraction, 3 ligands (MLT, NAG, SO4), 12 pockets (best druggability 0.68). MolNFT v1 #135763 on…
- 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.
| Volume (ų) | 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 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 846 Ų buried · 15 hydrogen bonds · protein-protein
- A–L · 255 Ų 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
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