Research workbench
Structural basis for eliciting a cytotoxic effect in HER2- overexpressing cancer cells via binding to the extracellular domain of HER2
Analyse Structural basis for eliciting a cytotoxic effect in HER2- overexpressing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HRM
- Type
- protein
- Length
- 547 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Domain I of receptor tyrosine-protein kinase erbb-2; Designed ankyrin repeat protein 9_26
- EC
- 2.7.10.1
- UniProt
- P04626
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Domain I of receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 166 | 11% helix, 24% strand | P04626 |
| A | Domain I of receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 139 | 11% helix, 18% strand | P04626 |
| B | Designed ankyrin repeat protein 9_26 | protein | 123 | 52% helix, 0% strand | — |
| D | Designed ankyrin repeat protein 9_26 | protein | 119 | 48% helix, 0% strand | — |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.81 | 0.90 | 56 | empty |
| 2 | 188 | 0.79 | 0.93 | 40 | empty |
| 3 | 193 | 0.61 | 0.82 | 38 | empty |
| 4 | 115 | 0.47 | 0.79 | 20 | empty |
| 5 | 77 | 0.39 | 0.78 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–A · 421 Ų buried · 1 hydrogen bond · protein-protein
- C–B · 196 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 36 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4HRM · Structural Basis for Eliciting a Cytotoxic Effect in HER2-Overexpressing Cancer Cells via… · the same entry in another collection · chain C against C, 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 0.98
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 4HRM · PDBe 4HRM · UniProt P04626
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