MolNFT v1 · #153352 · protein
Complex structure of toripalimab-Fab and pd-1
6JBT · Programmed cell death protein 1: “Complex structure of toripalimab-Fab and pd-1”. X-ray diffraction, 2 ligands (NAG, FUC), 5 pockets (best druggability 0.42). MolNFT v1 #153352 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6JBT
- Type
- protein
- Length
- 546 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death protein 1; Heavy chain; Light chain
- UniProt
- Q15116
- Ligands
- NAG, FUC
- Pockets
- 5 · best druggability 0.42
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Programmed cell death protein 1 | protein | 111 | 3% helix, 58% strand | Q15116 |
| H | Heavy chain | protein | 217 | 6% helix, 53% strand | — |
| L | Light chain | protein | 218 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains F
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.42 | 0.76 | 23 | empty |
| 2 | 85 | 0.41 | 0.78 | 26 | empty |
| 3 | 111 | 0.40 | 0.76 | 20 | empty |
| 4 | 97 | 0.32 | 0.72 | 22 | empty |
| 5 | 76 | 0.32 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1838 Ų buried · 14 hydrogen bonds · protein-protein
- F–H · 597 Ų buried · 8 hydrogen bonds · protein-protein
- F–L · 335 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q15116
- Elsewhere: RCSB PDB 6JBT · PDBe 6JBT · UniProt Q15116
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