Research workbench
Crystal structure of the complex between mouse pd-1 mutant and pd-L2 igv domain
Analyse Crystal structure of the complex between mouse pd-1 mutant and pd-L2 igv domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RNK
- Type
- protein
- Length
- 216 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death protein 1; Programmed cell death 1 ligand 2
- UniProt
- Q02242, Q9WUL5
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Programmed cell death protein 1 | protein | 112 | 3% helix, 55% strand | Q02242 |
| B | Programmed cell death 1 ligand 2 | protein | 104 | 12% helix, 52% strand | Q9WUL5 |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.31 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1069 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3RNK · Crystal structure of the complex between mouse PD-1 mutant and PD-L2 IgV domain · 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 0.95
- Q9WUL5 · AlphaFold monomer V2.0 prediction for programmed cell death 1 ligand 2 (Q9WUL5) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q9WUL5
- Elsewhere: RCSB PDB 3RNK · PDBe 3RNK · UniProt Q02242 · UniProt Q9WUL5
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