MolNFT v1 · #153605 · protein
Crystal structure of Fab of a pd-1 monoclonal antibody MW11-H317 in complex with pd-1
6JJP · Heavy chain of MW11-H317: “Crystal structure of Fab of a pd-1 monoclonal antibody MW11-H317 in complex with pd-1”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 14 pockets (best druggability 0.82). MolNFT v1 #153605 on GenesisL1: 3D…
- PDB
- 6JJP
- Type
- protein
- Length
- 1,102 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of MW11-H317; Light chain of MW11-H317; Programmed cell death protein 1
- UniProt
- Q15116
- Ligands
- NAG, BMA, MAN, FUC
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Heavy chain of MW11-H317 | protein | 220 | 8% helix, 52% strand | — |
| B | Light chain of MW11-H317 | protein | 214 | 6% helix, 52% strand | — |
| C | Programmed cell death protein 1 | protein | 117 | 3% helix, 53% strand | Q15116 |
| E | Light chain of MW11-H317 | protein | 213 | 6% helix, 52% strand | — |
| F | Programmed cell death protein 1 | protein | 118 | 3% helix, 51% strand | Q15116 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, D, F
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, D
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, D
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.82 | 0.84 | 117 | empty |
| 2 | 208 | 0.68 | 0.86 | 24 | empty |
| 3 | 169 | 0.53 | 0.79 | 35 | empty |
| 4 | 141 | 0.51 | 0.80 | 26 | empty |
| 5 | 113 | 0.49 | 0.80 | 21 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1994 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1926 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 634 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 626 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 576 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6JJP · Crystal structure of Fab of a PD-1 monoclonal antibody MW11-h317 in complex with PD-1 · the same entry in another collection · chain F against F, TM-score 1.00
- Q15116 · AlphaFold monomer V2.0 prediction for programmed cell death protein 1 (Q15116) · a predicted model of the same protein · chain F against A, TM-score 0.96
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 6JJP · PDBe 6JJP · UniProt Q15116
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