Research workbench
Crystal structure of the complex between the EGFR kinase domain and a MIG6 peptide
Analyse Crystal structure of the complex between the EGFR kinase domain and a MIG6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RFD
- Type
- protein
- Length
- 605 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; Erbb receptor feedback inhibitor 1
- EC
- 2.7.10.1
- UniProt
- P00533, Q9UJM3
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 288 | 35% helix, 19% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 286 | 35% helix, 18% strand | P00533 |
| C | Erbb receptor feedback inhibitor 1 | protein | 16 | 0% helix, 13% strand | Q9UJM3 |
| D | Erbb receptor feedback inhibitor 1 | protein | 15 | 0% helix, 13% strand | Q9UJM3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.76 | 0.79 | 95 | SO4 |
| 2 | 336 | 0.67 | 0.81 | 53 | empty |
| 3 | 229 | 0.56 | 0.78 | 27 | empty |
| 4 | 242 | 0.53 | 0.76 | 20 | empty |
| 5 | 92 | 0.42 | 0.78 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–D · 731 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 729 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 611 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2RFD · Crystal structure of the complex between the EGFR kinase domain and a Mig6 peptide · the same entry in another collection · chain D against D, 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
- Q9UJM3 · AlphaFold monomer V2.0 prediction for erbb receptor feedback inhibitor 1 (Q9UJM3) · a predicted model of the same protein · chain D against A, TM-score 0.77
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 Q9UJM3
- Elsewhere: RCSB PDB 2RFD · PDBe 2RFD · UniProt P00533 · UniProt Q9UJM3
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