MolNFT v1 · #82893 · protein
Insulin receptor ectodomain construct comprising domains L1-cr in complex with human insulin, alpha-ct PEPTIDE(704-719) and Fab 83-7
3W11 · Insulin a chain: “Insulin receptor ectodomain construct comprising domains L1-cr in complex with human insulin, alpha-ct…”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 6 pockets (best druggability 0.47). MolNFT v1 #82893 on…
- PDB
- 3W11
- Type
- protein
- Length
- 567 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin a chain; Insulin B chain; Monoclonal antibody Fab 83-7 fragment - heavy chain…
- EC
- 2.7.10.1
- UniProt
- P01308, P06213
- Ligands
- NAG, BMA, MAN
- Pockets
- 6 · best druggability 0.47
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin a chain | protein | 21 | 67% helix, 0% strand | P01308 |
| B | Insulin B chain | protein | 15 | 80% helix, 0% strand | P01308 |
| C | Monoclonal antibody Fab 83-7 fragment - heavy chain | protein | 118 | 5% helix, 48% strand | — |
| D | Monoclonal antibody Fab 83-7 fragment - light chain | protein | 114 | 3% helix, 50% strand | — |
| E | Insulin receptor domains L1-cr (EC 2.7.10.1) | protein | 288 | 10% helix, 32% strand | P06213 |
| F | Insulin receptor alpha-ct peptide (EC 2.7.10.1) | protein | 11 | 73% helix, 0% strand | P06213 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains E, C, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.47 | 0.75 | 26 | empty |
| 2 | 91 | 0.46 | 0.81 | 23 | NAG |
| 3 | 132 | 0.44 | 0.77 | 24 | empty |
| 4 | 111 | 0.37 | 0.74 | 16 | empty |
| 5 | 56 | 0.26 | 0.73 | 25 | empty |
Interfaces
9 interfaces between chains.
- C–D · 872 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 496 Ų buried · 3 hydrogen bonds · protein-protein
- C–E · 492 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 407 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 395 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 18 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 3W11 · Insulin receptor ectodomain construct comprising domains L1-CR in complex with human… · the same entry in another collection · chain F against F, TM-score 1.00
- P06213 · AlphaFold monomer V2.0 prediction for insulin receptor (P06213) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 P01308
- Every structure of UniProt P06213
- Elsewhere: RCSB PDB 3W11 · PDBe 3W11 · UniProt P01308 · UniProt P06213
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