MolNFT v1 · #153623 · protein
Cryo-EM structure of the full-length human igf-1R in complex with insulin
6JK8 · Insulin-like growth factor 1 receptor: “Cryo-EM structure of the full-length human igf-1R in complex with insulin”. Electron microscopy, 2 ligands (NAG, MAN), 20 pockets (best druggability 0.85). MolNFT v1 #153623 on GenesisL1: 3D…
- PDB
- 6JK8
- Type
- protein
- Length
- 1,670 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-like growth factor 1 receptor; Insulin
- EC
- 2.7.10.1
- UniProt
- P08069, P01308
- Ligands
- NAG, MAN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 8% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin-like growth factor 1 receptor (EC 2.7.10.1) | protein | 823 | 8% helix, 30% strand | P08069 |
| B | Insulin-like growth factor 1 receptor (EC 2.7.10.1) | protein | 801 | 8% helix, 30% strand | P08069 |
| C | Insulin | protein | 21 | 38% helix, 0% strand | P01308 |
| D | Insulin | protein | 25 | 20% helix, 0% strand | P01308 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.85 | 0.93 | 58 | empty |
| 2 | 134 | 0.80 | 0.97 | 35 | empty |
| 3 | 1137 | 0.79 | 0.81 | 86 | empty |
| 4 | 825 | 0.77 | 0.81 | 87 | empty |
| 5 | 152 | 0.76 | 0.93 | 43 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1341 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 561 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 540 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 455 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 353 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 6JK8 · Cryo-EM structure of the full-length human IGF-1R in complex with insulin · 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
- Every structure of UniProt P01308
- Elsewhere: RCSB PDB 6JK8 · PDBe 6JK8 · UniProt P08069 · UniProt P01308
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