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Structure of ig-like V-type domian of mouse programmed cell death 1 ligand 1 (pd-L1)
Analyse Structure of ig-like V-type domian of mouse programmed cell death 1 ligand 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SRU
- Type
- protein
- Length
- 1,146 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death 1 ligand 1
- UniProt
- Q9EP73
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 7 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, H | Programmed cell death 1 ligand 1 | protein | 116 | 9% helix, 43% strand | Q9EP73 |
| C | Programmed cell death 1 ligand 1 | protein | 115 | 9% helix, 44% strand | Q9EP73 |
| D | Programmed cell death 1 ligand 1 | protein | 114 | 9% helix, 45% strand | Q9EP73 |
| E | Programmed cell death 1 ligand 1 | protein | 115 | 9% helix, 43% strand | Q9EP73 |
| G | Programmed cell death 1 ligand 1 | protein | 114 | 9% helix, 44% strand | Q9EP73 |
| I | Programmed cell death 1 ligand 1 | protein | 111 | 6% helix, 45% strand | Q9EP73 |
| J | Programmed cell death 1 ligand 1 | protein | 113 | 10% helix, 45% strand | Q9EP73 |
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.73 | 0.77 | 98 | empty |
| 2 | 727 | 0.67 | 0.75 | 67 | empty |
| 3 | 558 | 0.64 | 0.76 | 64 | empty |
| 4 | 247 | 0.52 | 0.76 | 25 | empty |
| 5 | 176 | 0.51 | 0.78 | 24 | empty |
Interfaces
16 interfaces between chains.
- D–G · 677 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 676 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 633 Ų buried · 8 hydrogen bonds · protein-protein
- D–I · 632 Ų buried · 6 hydrogen bonds · protein-protein
- C–H · 262 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6SRU · Structure of Ig-like V-type domian of mouse Programmed cell death 1 ligand 1 (PD-L1) · the same entry in another collection · chain J against J, TM-score 1.00
- Q9EP73 · AlphaFold monomer V2.0 prediction for programmed cell death 1 ligand 1 (Q9EP73) · a predicted model of the same protein · chain I against A, TM-score 0.97
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 Q9EP73
- Elsewhere: RCSB PDB 6SRU · PDBe 6SRU · UniProt Q9EP73
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