Research workbench
Structure of a dimeric anti-HER2 single domain antibody
Analyse Structure of a dimeric anti-HER2 single domain antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QYC
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vh domain of IgG molecule
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vh domain of IgG molecule | protein | 125 | 7% helix, 46% strand | — |
| B | Vh domain of IgG molecule | protein | 123 | 5% helix, 46% strand | — |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.46 | 0.78 | 19 | empty |
| 2 | 72 | 0.41 | 0.80 | 14 | empty |
| 3 | 72 | 0.34 | 0.76 | 10 | empty |
| 4 | 53 | 0.24 | 0.72 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1184 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3QYC · Structure of a dimeric anti-HER2 single domain antibody · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3QYC · PDBe 3QYC
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