MolNFT v2 · #116941 · protein
Crystal Structure of Pembrolizumab, a full length IgG4 antibody
5DK3: “Crystal Structure of Pembrolizumab, a full length IgG4 antibody”. X-ray diffraction at 2.28, 7 ligands (NAG, MAN, GLC). MolNFT v2 #116941 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DK3
- Type
- protein
- Length
- 1,315 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.28
- Source
- Homo sapiens
- Ligands
- NAG, MAN, GLC, FRU, BMA, FUC, SO4
Structure
x-ray diffraction · resolution 2.28 · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | — | protein | 218 | — | — |
| B | — | protein | 441 | — | — |
| G | — | protein | 438 | — | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains B, G
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B, G
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains B, G
- FRU · beta-D-fructofuranose · sugar · 3 copies · chains B, G
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B, G
- FUC · alpha-L-fucopyranose · sugar · chains B, G
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5DK3 · Crystal structure of pembrolizumab, a full length IGG4 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 5DK3 · PDBe 5DK3
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