MolNFT v1 · #124830 · protein
Insulin receptor ectodomain construct comprising domains L1,CR,L2, fniii-1 and alphact peptide in complex with bovine insulin and Fab 83-14 (revised structure)
5KQV: “Insulin receptor ectodomain construct comprising domains L1,CR,L2, fniii-1 and alphact peptide in complex…”. X-ray diffraction, 2 ligands (NAG, FUC), 20 pockets (best druggability 0.86). MolNFT v1 #124830 on GenesisL1: 3D structure…
- PDB
- 5KQV
- Type
- protein
- Length
- 2,120 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin; Monoclonal antibody Fab 83-14 - heavy chain; Monoclonal antibody Fab 83-14…
- EC
- 2.7.10.1
- UniProt
- P01317, P06213
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 10% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | Insulin | protein | 21 | 43% helix, 0% strand | P01317 |
| B, J | Insulin | protein | 17 | 71% helix, 0% strand | P01317 |
| C | Monoclonal antibody Fab 83-14 - heavy chain | protein | 211 | 6% helix, 52% strand | — |
| D, Q | Monoclonal antibody Fab 83-14 - light chain | protein | 214 | 6% helix, 50% strand | — |
| E | Insulin RECEPTOR,INSULIN receptor (EC 2.7.10.1) | protein | 593 | 10% helix, 31% strand | P06213 |
| F | Insulin RECEPTOR,INSULIN receptor (EC 2.7.10.1) | protein | 592 | 10% helix, 31% strand | P06213 |
| P | Monoclonal antibody Fab 83-14 - heavy chain | protein | 220 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains E, F
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.86 | 0.87 | 93 | empty |
| 2 | 287 | 0.58 | 0.77 | 38 | empty |
| 3 | 71 | 0.58 | 0.89 | 22 | empty |
| 4 | 200 | 0.58 | 0.80 | 26 | empty |
| 5 | 252 | 0.56 | 0.77 | 32 | empty |
Interfaces
13 interfaces between chains.
- C–D · 1857 Ų buried · 11 hydrogen bonds · protein-protein
- P–Q · 1848 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1398 Ų buried · 18 hydrogen bonds · protein-protein
- F–P · 573 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 561 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 49 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5KQV · Insulin receptor ectodomain construct comprising domains L1,CR,L2, FnIII-1 and alphaCT… · the same entry in another collection · chain Q against Q, TM-score 1.00
- P06213 · AlphaFold monomer V2.0 prediction for insulin receptor (P06213) · a predicted model of the same protein · chain F against A, TM-score 0.60
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 P01317
- Every structure of UniProt P06213
- Elsewhere: RCSB PDB 5KQV · PDBe 5KQV · UniProt P01317 · UniProt P06213
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