MolNFT v1 · #145106 · protein
Insulin receptor ectodomain in complex with two insulin molecules - C1 symmetry
6CEB: “Insulin receptor ectodomain in complex with two insulin molecules - C1 symmetry”. Electron microscopy, 3 ligands (NAG, FUC, BMA), 20 pockets (best druggability 0.76). MolNFT v1 #145106 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6CEB
- Type
- protein
- Length
- 1,406 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin receptor; Insulin a chain; Insulin B chain
- EC
- 2.7.10.1
- UniProt
- P06213, P01308, P01318
- Ligands
- NAG, FUC, BMA
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 5 distinct chains · 12% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin receptor (EC 2.7.10.1) | protein | 682 | 9% helix, 29% strand | P06213 |
| B | Insulin receptor (EC 2.7.10.1) | protein | 562 | 9% helix, 27% strand | P06213 |
| M, P | Insulin receptor (EC 2.7.10.1) | protein | 30 | 73% helix, 0% strand | P06213 |
| K, N | Insulin a chain | protein | 21 | 48% helix, 0% strand | P01308 |
| L, O | Insulin B chain | protein | 30 | 40% helix, 0% strand | P01318 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B, O, L
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.76 | 0.97 | 22 | empty |
| 2 | 68 | 0.75 | 0.98 | 28 | empty |
| 3 | 363 | 0.75 | 0.85 | 50 | empty |
| 4 | 358 | 0.74 | 0.85 | 59 | empty |
| 5 | 78 | 0.74 | 0.96 | 27 | empty |
Interfaces
17 interfaces between chains.
- A–P · 923 Ų buried · 4 hydrogen bonds · protein-protein
- B–M · 892 Ų buried · 4 hydrogen bonds · protein-protein
- K–L · 604 Ų buried · 9 hydrogen bonds · protein-protein
- N–O · 598 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 535 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6CEB · Insulin Receptor ectodomain in complex with two insulin molecules - C1 symmetry · the same entry in another collection · chain P against P, TM-score 1.00
- P06213 · AlphaFold monomer V2.0 prediction for insulin receptor (P06213) · a predicted model of the same protein · chain M against A, TM-score 0.65
- P01318 · AlphaFold monomer V2.0 prediction for insulin (P01318) · a predicted model of the same protein · chain L against A, TM-score 0.40
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 P06213
- Every structure of UniProt P01308
- Every structure of UniProt P01318
- Elsewhere: RCSB PDB 6CEB · PDBe 6CEB · UniProt P06213 · UniProt P01308 · UniProt P01318
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