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Crystal structure of extracellular domain of human HER2 complexed with herceptin Fab
Analyse Crystal structure of extracellular domain of human HER2 complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N8Z
- Type
- protein
- Length
- 1,015 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Herceptin Fab (antibody) - light chain; Herceptin Fab (antibody) - heavy chain; Receptor…
- EC
- 2.7.1.112
- UniProt
- P04626
- Ligands
- NAG, SO4
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Herceptin Fab (antibody) - light chain | protein | 214 | 6% helix, 50% strand | — |
| B | Herceptin Fab (antibody) - heavy chain | protein | 220 | 8% helix, 51% strand | — |
| C | Receptor protein-tyrosine kinase erbb-2 (EC 2.7.1.112) | protein | 581 | 10% helix, 26% strand | P04626 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C
- SO4 · Sulfate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.70 | 0.79 | 71 | empty |
| 2 | 664 | 0.64 | 0.74 | 60 | empty |
| 3 | 117 | 0.46 | 0.79 | 27 | empty |
| 4 | 125 | 0.41 | 0.75 | 27 | empty |
| 5 | 107 | 0.41 | 0.76 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1823 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 430 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 414 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1N8Z · Crystal structure of extracellular domain of human HER2 complexed with Herceptin Fab · 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 C 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 P04626
- Elsewhere: RCSB PDB 1N8Z · PDBe 1N8Z · UniProt P04626
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