Research workbench
Crystal structure of the complex between the extracellular domains of mouse pd-1 mutant and human pd-L1
Analyse Crystal structure of the complex between the extracellular domains of mouse… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SBW
- Type
- protein
- Length
- 432 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death protein 1; Programmed cell death 1 ligand 1
- UniProt
- Q02242, Q9NZQ7
- Pockets
- 3 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Programmed cell death protein 1 | protein | 112 | 3% helix, 54% strand | Q02242 |
| C | Programmed cell death 1 ligand 1 | protein | 208 | 5% helix, 55% strand | Q9NZQ7 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.34 | 0.78 | 12 | empty |
| 2 | 66 | 0.31 | 0.74 | 14 | empty |
| 3 | 57 | 0.27 | 0.74 | 16 | empty |
Interfaces
2 interfaces between chains.
- B–C · 956 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 578 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3SBW · Crystal structure of the complex between the extracellular domains of mouse PD-1 mutant… · the same entry in another collection · chain A against A, TM-score 1.00
- Q02242 · AlphaFold monomer V2.0 prediction for programmed cell death protein 1 (Q02242) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q02242
- Every structure of UniProt Q9NZQ7
- Elsewhere: RCSB PDB 3SBW · PDBe 3SBW · UniProt Q02242 · UniProt Q9NZQ7
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