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
- 4HRN
- Type
- protein
- Length
- 385 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Designed ankyrin repeat protein H10-2-G; Receptor tyrosine-protein kinase erbb-2
- EC
- 2.7.10.1
- UniProt
- P04626
- Pockets
- 1 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Designed ankyrin repeat protein H10-2-G | protein | 121 | 55% helix, 0% strand | — |
| B | Designed ankyrin repeat protein H10-2-G | protein | 123 | 57% helix, 0% strand | — |
| C | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 71 | 0% helix, 34% strand | P04626 |
| D | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 70 | 0% helix, 34% strand | P04626 |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.66 | 0.78 | 60 | empty |
Interfaces
6 interfaces between chains.
- A–D · 788 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 729 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 598 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 367 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4HRN · Structural Basis for Eliciting a Cytotoxic Effect in HER2-Overexpressing Cancer Cells via… · 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 0.96
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 4HRN · PDBe 4HRN · UniProt P04626
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