MolNFT v1 · #112831 · protein
Structure of the human insulin receptor ectodomain, irdeltabeta construct, in complex with four Fab molecules
4ZXB · Fab 83-7 heavy chain: “Structure of the human insulin receptor ectodomain, irdeltabeta construct, in complex with four Fab molecules”. X-ray diffraction, 4 ligands (NAG, FUC, BMA), 20 pockets (best druggability 0.64). MolNFT v1…
- PDB
- 4ZXB
- Type
- protein
- Length
- 1,601 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 83-7 heavy chain; Fab 83-7 light chain; Fab 83-14 heavy chain; Fab 83-14 light chain…
- UniProt
- U5LP42, P01837, P01865, A2P1G9, P06213
- Ligands
- NAG, FUC, BMA, MAN
- Pockets
- 20 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab 83-7 heavy chain | protein | 214 | 9% helix, 50% strand | U5LP42 |
| B | Fab 83-7 light chain | protein | 218 | 6% helix, 55% strand | P01837 |
| C | Fab 83-14 heavy chain | protein | 187 | 8% helix, 56% strand | P01865 |
| D | Fab 83-14 light chain | protein | 182 | 5% helix, 44% strand | A2P1G9 |
| E | Insulin receptor | protein | 800 | 10% helix, 34% strand | P06213 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains E, A
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains E
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 637 | 0.64 | 0.75 | 52 | empty |
| 2 | 405 | 0.58 | 0.75 | 51 | empty |
| 3 | 235 | 0.55 | 0.78 | 25 | empty |
| 4 | 152 | 0.52 | 0.80 | 24 | empty |
| 5 | 193 | 0.45 | 0.74 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1833 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1531 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 639 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 530 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 499 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 4ZXB · Structure of the human insulin receptor ectodomain, IRDeltabeta construct, in complex… · the same entry in another collection · chain E against E, 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 0.65
- P01837 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01837) · a predicted model of the same protein · chain B against A, TM-score 0.48
- P01865 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, membrane-bound form… · a predicted model of the same protein · chain C against A, TM-score 0.45
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 U5LP42
- Every structure of UniProt P01837
- Every structure of UniProt P01865
- Every structure of UniProt A2P1G9
- Every structure of UniProt P06213
- Elsewhere: RCSB PDB 4ZXB · PDBe 4ZXB · UniProt U5LP42 · UniProt P01837 · UniProt P01865 · UniProt A2P1G9 · UniProt P06213
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