Research workbench
Crystal structure of human pd-L1 in complex with high affinity pd-1 mutant
Analyse Crystal structure of human pd-L1 in complex with high affinity pd-1 mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IUS
- Type
- protein
- Length
- 657 residues
- Chains
- 4
- 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
- Q15116, Q9NZQ7
- Ligands
- CL
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Programmed cell death protein 1 | protein | 117 | 5% helix, 50% strand | Q15116 |
| B | Programmed cell death protein 1 | protein | 115 | 3% helix, 51% strand | Q15116 |
| C | Programmed cell death 1 ligand 1 | protein | 214 | 5% helix, 53% strand | Q9NZQ7 |
| D | Programmed cell death 1 ligand 1 | protein | 211 | 6% helix, 55% strand | Q9NZQ7 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.65 | 0.77 | 64 | empty |
| 2 | 284 | 0.57 | 0.77 | 38 | empty |
| 3 | 150 | 0.44 | 0.76 | 24 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2082 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 889 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 871 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 69 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5IUS · Crystal structure of human PD-L1 in complex with high affinity PD-1 mutant · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.92
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
- Every structure of UniProt Q9NZQ7
- Elsewhere: RCSB PDB 5IUS · PDBe 5IUS · UniProt Q15116 · UniProt Q9NZQ7
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