Research workbench
Crystal structure of pembrolizumab, a full length IGG4 antibody
Analyse Crystal structure of pembrolizumab, a full length IGG4 antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DK3
- Type
- protein
- Length
- 1,315 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain; Heavy chain
- Ligands
- NAG, MAN, GLC, FRU, BMA, FUC, SO4
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Light chain | protein | 218 | 6% helix, 51% strand | — |
| B | Heavy chain | protein | 441 | 7% helix, 49% strand | — |
| G | Heavy chain | protein | 438 | 9% helix, 49% strand | — |
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.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.70 | 0.81 | 50 | empty |
| 2 | 407 | 0.63 | 0.78 | 52 | empty |
| 3 | 249 | 0.59 | 0.79 | 42 | empty |
| 4 | 53 | 0.58 | 0.91 | 20 | empty |
| 5 | 491 | 0.58 | 0.73 | 51 | SO4 |
Interfaces
5 interfaces between chains.
- B–G · 2335 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1838 Ų buried · 14 hydrogen bonds · protein-protein
- F–G · 1790 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 264 Ų buried · 1 hydrogen bond · protein-protein
- A–G · 27 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 1 glycan (disulfide, N-glycosylation).
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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