Research workbench
Structure of the HER2/HER3/NRG1B heterodimer extracellular domain
Analyse Structure of the HER2/HER3/NRG1B heterodimer extracellular domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MN5
- Type
- protein
- Length
- 1,213 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor tyrosine-protein kinase erbb-3; Isoform 6 of pro-neuregulin-1, membrane-bound…
- EC
- 2.7.10.1
- UniProt
- P21860, P04626
- Ligands
- NAG, BMA, MAN
- Pockets
- 13 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 10% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1) | protein | 585 | 11% helix, 28% strand | P21860 |
| H | Isoform 6 of pro-neuregulin-1, membrane-bound isoform | protein | 49 | 6% helix, 33% strand | — |
| B | Receptor tyrosine-protein kinase erbb-2, MALTOSE/MALTODEXTRIN-binding periplasmic protein (EC 2.7.10.1) | protein | 579 | 10% helix, 25% strand | P04626 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.79 | 0.82 | 86 | empty |
| 2 | 755 | 0.74 | 0.80 | 91 | empty |
| 3 | 389 | 0.64 | 0.78 | 42 | empty |
| 4 | 132 | 0.50 | 0.79 | 25 | empty |
| 5 | 141 | 0.48 | 0.78 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–H · 1477 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1074 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 7MN5 · Structure of the HER2/HER3/NRG1b Heterodimer Extracellular Domain · the same entry in another collection · chain A against A, TM-score 1.00
- P04626 · AlphaFold monomer V2.0 prediction for receptor tyrosine-protein kinase erbb-2 (P04626) · a predicted model of the same protein · chain B against A, TM-score 0.95
- 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 0.51
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 P04626
- Elsewhere: RCSB PDB 7MN5 · PDBe 7MN5 · UniProt P21860 · UniProt P04626
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