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A general strategy for the generation of human antibody variable domains with increased aggregation resistance
Analyse A general strategy for the generation of human antibody variable domains with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UPC
- Type
- protein
- Length
- 1,130 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Homo sapiens
- Molecule
- heavy chain variable domain
- Pockets
- 13 · best druggability 0.89
Structure
x-ray diffraction · resolution 2.8 · 1 distinct chain · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | heavy chain variable domain | protein | 113 | 5% helix, 48% strand | — |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · 3 copies · chains E, G, H, I
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B, I, C, D
- PGE · Triethylene glycol · additive · chains B, C
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.89 | 0.90 | 123 | 1PE, PGE, PEG, PG4 |
| 2 | 954 | 0.86 | 0.87 | 93 | PG4 |
| 3 | 66 | 0.42 | 0.81 | 18 | empty |
| 4 | 68 | 0.42 | 0.81 | 19 | empty |
| 5 | 77 | 0.41 | 0.79 | 17 | empty |
Interfaces
17 interfaces between chains.
- C–D · 1719 Ų buried · 39 hydrogen bonds · protein-protein
- F–J · 1706 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 1700 Ų buried · 40 hydrogen bonds · protein-protein
- G–H · 1693 Ų buried · 35 hydrogen bonds · protein-protein
- E–I · 1672 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3UPC · A general strategy for the generation of human antibody variable domains with increased… · 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 3UPC · PDBe 3UPC
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