Research workbench
Structure of the human insulin receptor ectodomain, irdeltabeta construct, in complex with four Fab molecules
Analyse Structure of the human insulin receptor ectodomain, irdeltabeta construct, in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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