Research workbench
The complex structure of extracellular domain of EGFR with repebody (RAC1).
Analyse The complex structure of extracellular domain of EGFR with repebody (RAC1). in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UIP
- Type
- protein
- Length
- 850 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; Repebody (RAC1)
- UniProt
- P00533, E0ACT6, Q4G1L3
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor | protein | 612 | 10% helix, 25% strand | P00533 |
| B | Repebody (RAC1) | protein | 238 | 16% helix, 13% strand | E0ACT6, Q4G1L3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.65 | 0.85 | 33 | empty |
| 2 | 308 | 0.63 | 0.80 | 54 | empty |
| 3 | 52 | 0.51 | 0.88 | 14 | empty |
| 4 | 113 | 0.50 | 0.81 | 33 | empty |
| 5 | 55 | 0.37 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1083 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4UIP · The complex structure of extracellular domain of EGFR with Repebody (rAC1). · 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 0.93
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
- Every structure of UniProt E0ACT6
- Every structure of UniProt Q4G1L3
- Elsewhere: RCSB PDB 4UIP · PDBe 4UIP · UniProt P00533 · UniProt E0ACT6 · UniProt Q4G1L3
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