Research workbench
Crystal structure of an EGFR/HER3 kinase domain heterodimer containing the cancer-associated HER3-E909G mutation
Analyse Crystal structure of an EGFR/HER3 kinase domain heterodimer containing the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RIY
- Type
- protein
- Length
- 1,134 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor tyrosine-protein kinase erbb-3; Epidermal growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P21860, P00533
- Ligands
- ANP, ADP, MG
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1) | protein | 269 | 38% helix, 19% strand | P21860 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 293 | 34% helix, 20% strand | P00533 |
| C | Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1) | protein | 275 | 40% helix, 17% strand | P21860 |
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 297 | 34% helix, 19% strand | P00533 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, C
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.72 | 0.78 | 58 | empty |
| 2 | 373 | 0.72 | 0.83 | 46 | ANP, MG |
| 3 | 334 | 0.66 | 0.81 | 39 | ADP, MG |
| 4 | 352 | 0.66 | 0.80 | 41 | ADP, MG |
| 5 | 318 | 0.66 | 0.81 | 33 | ANP, MG |
Interfaces
3 interfaces between chains.
- A–B · 1470 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1468 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 431 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4RIY · Crystal structure of an EGFR/HER3 kinase domain heterodimer containing the… · the same entry in another collection · chain D against D, TM-score 1.00
- P21860 · AlphaFold monomer V2.0 prediction for receptor tyrosine-protein kinase erbb-3 (P21860) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain D 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 P21860
- Every structure of UniProt P00533
- Elsewhere: RCSB PDB 4RIY · PDBe 4RIY · UniProt P21860 · UniProt P00533
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