Research workbench
Structure of the HER2/HER3/NRG1B heterodimer extracellular domain bound to trastuzumab Fab
Analyse Structure of the HER2/HER3/NRG1B heterodimer extracellular domain bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MN8
- Type
- protein
- Length
- 1,661 residues
- Chains
- 5
- 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
- 20 · best druggability 0.77
Structure
electron microscopy · 5 distinct chains · 9% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1) | protein | 599 | 11% helix, 29% strand | P21860 |
| H | Isoform 6 of pro-neuregulin-1, membrane-bound isoform | protein | 49 | 8% helix, 35% strand | — |
| B | Receptor tyrosine-protein kinase erbb-2, MALTOSE/MALTODEXTRIN-binding periplasmic protein (EC 2.7.10.1) | protein | 579 | 10% helix, 26% strand | P04626 |
| C | Trastuzumab Fab light chain | protein | 214 | 6% helix, 50% strand | — |
| D | Trastuzumab Fab heavy chain | protein | 220 | 7% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · chains B
- MAN · alpha-D-mannopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.77 | 0.80 | 88 | empty |
| 2 | 915 | 0.76 | 0.79 | 100 | empty |
| 3 | 834 | 0.75 | 0.79 | 93 | NAG |
| 4 | 63 | 0.72 | 0.98 | 18 | empty |
| 5 | 441 | 0.62 | 0.76 | 41 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1925 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1800 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 1422 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 485 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 422 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 7MN8 · Structure of the HER2/HER3/NRG1b Heterodimer Extracellular Domain bound to Trastuzumab Fab · the same entry in another collection · chain H against H, 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 0.96
- 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 0.50
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 7MN8 · PDBe 7MN8 · UniProt P21860 · UniProt P04626
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