Research workbench
Site-specific lysine arylation as an alternative bioconjugation strategy for chemically programmed antibodies and antibody-drug conjugates
Analyse Site-specific lysine arylation as an alternative bioconjugation strategy for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U85
- Type
- protein
- Length
- 434 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab heavy chain; Antibody Fab light chain
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody Fab heavy chain | protein | 216 | 7% helix, 52% strand | — |
| L | Antibody Fab light chain | protein | 218 | 7% helix, 46% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.60 | 0.74 | 74 | empty |
| 2 | 159 | 0.44 | 0.75 | 31 | empty |
| 3 | 90 | 0.38 | 0.76 | 27 | empty |
| 4 | 53 | 0.26 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- H–L · 1853 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6U85 · Site-specific lysine arylation as an alternative bioconjugation strategy for chemically… · the same entry in another collection · chain H against H, 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 6U85 · PDBe 6U85
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