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Crystallographic trimer of HER2 extracellular regions in complex with tryptophan-rich antibody fragment
Analyse Crystallographic trimer of HER2 extracellular regions in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N85
- Type
- protein
- Length
- 1,033 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor tyrosine-protein kinase erbb-2; FAB37 light chain; FAB37 heavy chain
- EC
- 2.7.10.1
- UniProt
- P04626
- Ligands
- NAG, BMA, FUC, SO4, CL
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 605 | 10% helix, 24% strand | P04626 |
| L | FAB37 light chain | protein | 214 | 6% helix, 51% strand | — |
| H | FAB37 heavy chain | protein | 214 | 3% helix, 55% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 16 copies · chains A, H, L
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.72 | 0.78 | 94 | NAG, SO4 |
| 2 | 457 | 0.57 | 0.73 | 56 | empty |
| 3 | 60 | 0.50 | 0.86 | 21 | empty |
| 4 | 140 | 0.48 | 0.78 | 26 | empty |
| 5 | 132 | 0.44 | 0.77 | 25 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1829 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 881 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 311 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3N85 · Crystallographic trimer of HER2 extracellular regions in complex with tryptophan-rich… · 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 A against A, TM-score 0.91
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 P04626
- Elsewhere: RCSB PDB 3N85 · PDBe 3N85 · UniProt P04626
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