Research workbench
Insights into erbb signaling from the structure of the ERBB2- pertuzumab complex
Analyse Insights into erbb signaling from the structure of the ERBB2- pertuzumab complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S78
- Type
- protein
- Length
- 1,995 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor protein-tyrosine kinase erbb-2; Pertuzumab Fab light chain; Pertuzumab Fab heavy…
- EC
- 2.7.1.112
- UniProt
- P04626
- Ligands
- NAG, BMA
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor protein-tyrosine kinase erbb-2 (EC 2.7.1.112) | protein | 555 | 10% helix, 24% strand | P04626 |
| B | Receptor protein-tyrosine kinase erbb-2 (EC 2.7.1.112) | protein | 568 | 11% helix, 25% strand | P04626 |
| C, E | Pertuzumab Fab light chain | protein | 214 | 1% helix, 42% strand | — |
| D, F | Pertuzumab Fab heavy chain | protein | 222 | 7% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.78 | 0.80 | 87 | empty |
| 2 | 811 | 0.76 | 0.80 | 70 | empty |
| 3 | 753 | 0.75 | 0.80 | 74 | empty |
| 4 | 277 | 0.61 | 0.80 | 36 | empty |
| 5 | 236 | 0.61 | 0.80 | 37 | empty |
Interfaces
7 interfaces between chains.
- C–D · 2072 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1960 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 981 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 966 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 433 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 1S78 · Insights into ErbB signaling from the structure of the ErbB2-pertuzumab complex · the same entry in another collection · chain F against F, 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 0.98
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 1S78 · PDBe 1S78 · UniProt P04626
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