Research workbench
Structure of the HER3 (ERBB3) extracellular domain
Analyse Structure of the HER3 (ERBB3) extracellular domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M6B
- Type
- protein
- Length
- 1,133 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor protein-tyrosine kinase erbb-3
- EC
- 2.7.10.1
- UniProt
- P21860
- Ligands
- NAG, SO4
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor protein-tyrosine kinase erbb-3 (EC 2.7.10.1) | protein | 549 | 8% helix, 28% strand | P21860 |
| B | Receptor protein-tyrosine kinase erbb-3 (EC 2.7.10.1) | protein | 584 | 8% helix, 29% strand | P21860 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.74 | 0.79 | 119 | NAG |
| 2 | 225 | 0.59 | 0.81 | 35 | empty |
| 3 | 237 | 0.56 | 0.78 | 41 | NAG |
| 4 | 80 | 0.35 | 0.76 | 23 | empty |
| 5 | 57 | 0.33 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 885 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 1M6B · Structure of the HER3 (ERBB3) Extracellular Domain · the same entry in another collection · chain A against A, 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 0.88
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
- Elsewhere: RCSB PDB 1M6B · PDBe 1M6B · UniProt P21860
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