Research workbench
Crystal structure of pd-L1 complexed with atezolizumab Fab at 2.9A
Analyse Crystal structure of pd-L1 complexed with atezolizumab Fab at 2.9A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XXY
- Type
- protein
- Length
- 518 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of atezolizumab Fab; Light chain of atezolizumab Fab; Programmed cell death 1…
- UniProt
- Q9NZQ7
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of atezolizumab Fab | protein | 208 | 1% helix, 50% strand | — |
| L | Light chain of atezolizumab Fab | protein | 211 | 5% helix, 52% strand | — |
| A | Programmed cell death 1 ligand 1 | protein | 99 | 7% helix, 53% strand | Q9NZQ7 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.64 | 0.74 | 68 | empty |
| 2 | 71 | 0.33 | 0.76 | 19 | empty |
| 3 | 51 | 0.29 | 0.75 | 9 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1707 Ų buried · 14 hydrogen bonds · protein-protein
- H–A · 848 Ų buried · 20 hydrogen bonds · protein-protein
- L–A · 272 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5XXY · Crystal structure of PD-L1 complexed with atezolizumab fab at 2.9A · 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 5XXY · PDBe 5XXY · UniProt Q9NZQ7
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