Research workbench
Crystal structure of human pd-L1 with monoclonal antibody avelumab
Analyse Crystal structure of human pd-L1 with monoclonal antibody avelumab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GRJ
- Type
- protein
- Length
- 439 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Avelumab H chain; Avelumab L chain; Programmed cell death 1 ligand 1
- UniProt
- Q9NZQ7
- Pockets
- 3 · best druggability 0.37
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Avelumab H chain | protein | 118 | 3% helix, 50% strand | — |
| L | Avelumab L chain | protein | 108 | 0% helix, 46% strand | — |
| A | Programmed cell death 1 ligand 1 | protein | 213 | 3% 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 | 79 | 0.37 | 0.77 | 19 | empty |
| 2 | 91 | 0.36 | 0.75 | 21 | empty |
| 3 | 80 | 0.30 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 729 Ų buried · 6 hydrogen bonds · protein-protein
- H–A · 690 Ų buried · 13 hydrogen bonds · protein-protein
- L–A · 306 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5GRJ · Crystal structure of human PD-L1 with monoclonal antibody avelumab · the same entry in another collection · chain H against H, TM-score 1.00
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 Q9NZQ7
- Elsewhere: RCSB PDB 5GRJ · PDBe 5GRJ · UniProt Q9NZQ7
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