Research workbench
The complex structure of extracellular domain of EGFR and GC1118A
Analyse The complex structure of extracellular domain of EGFR and GC1118A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UV7
- Type
- protein
- Length
- 1,030 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; GC1118A
- EC
- 2.7.10.1
- UniProt
- P00533
- Ligands
- NAG, BMA
- Pockets
- 13 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 596 | 12% helix, 27% strand | P00533 |
| H | GC1118A | protein | 218 | 11% helix, 49% strand | — |
| L | GC1118A | protein | 216 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 298 | 0.60 | 0.78 | 43 | empty |
| 2 | 163 | 0.43 | 0.74 | 32 | empty |
| 3 | 60 | 0.42 | 0.82 | 18 | empty |
| 4 | 101 | 0.40 | 0.76 | 22 | empty |
| 5 | 56 | 0.38 | 0.80 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1938 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 586 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 191 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4UV7 · The complex structure of extracellular domain of EGFR and GC1118A · the same entry in another collection · chain A against A, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P00533
- Elsewhere: RCSB PDB 4UV7 · PDBe 4UV7 · UniProt P00533
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