Research workbench
Structure of the extracellular domain of human epidermal growth factor (EGF) receptor in an inactive (low pH) complex with EGF.
Analyse Structure of the extracellular domain of human epidermal growth factor (EGF)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NQL
- Type
- protein
- Length
- 660 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; Epidermal growth factor
- UniProt
- P01133
- Ligands
- NAG, BMA
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor | protein | 612 | 12% helix, 25% strand | — |
| B | Epidermal growth factor | protein | 48 | 0% helix, 40% strand | P01133 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.71 | 0.77 | 99 | empty |
| 2 | 74 | 0.32 | 0.75 | 17 | empty |
| 3 | 86 | 0.32 | 0.73 | 16 | empty |
| 4 | 76 | 0.31 | 0.73 | 21 | empty |
| 5 | 63 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 830 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 7 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 1NQL · Structure of the extracellular domain of human epidermal growth factor (EGF) receptor in… · the same entry in another collection · chain A against A, TM-score 1.00
- P01133 · AlphaFold monomer V2.0 prediction for pro-epidermal growth factor (P01133) · a predicted model of the same protein · chain B against A, TM-score 0.66
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 P01133
- Elsewhere: RCSB PDB 1NQL · PDBe 1NQL · UniProt P01133
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