Research workbench
HuA21-scFv in complex with the extracellular domain(ECD) of HER2
Analyse HuA21-scFv in complex with the extracellular domain(ECD) of HER2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J71
- Type
- protein
- Length
- 851 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.918
- Source
- Homo sapiens
- Molecule
- Receptor tyrosine-protein kinase erbB-2; anti-HER2 humanized antibody HuA21
- EC
- 2.7.10.1
- UniProt
- P04626
- Ligands
- BMA, NAG
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · resolution 2.918 · 2 distinct chains · 8% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor tyrosine-protein kinase erbB-2 (EC 2.7.10.1) | protein | 618 | 9% helix, 23% strand | P04626 |
| B | anti-HER2 humanized antibody HuA21 | protein | 233 | 6% helix, 49% strand | — |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.64 | 0.77 | 59 | empty |
| 2 | 315 | 0.57 | 0.76 | 43 | empty |
| 3 | 173 | 0.54 | 0.79 | 23 | empty |
| 4 | 114 | 0.42 | 0.77 | 23 | empty |
| 5 | 93 | 0.36 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 936 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6J71 · HUA21-scfv in complex with the extracellular DOMAIN(ECD) of HER2 · 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 0.99
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 6J71 · PDBe 6J71 · UniProt P04626
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.