Research workbench
Crystal structure of alpn-202 (engineered CD80 vigd) in complex with pd-L1
Analyse Crystal structure of alpn-202 (engineered CD80 vigd) in complex with pd-L1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TPS
- Type
- protein
- Length
- 621 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-lymphocyte activation antigen CD80; Programmed cell death 1 ligand 1
- UniProt
- P33681, Q9NZQ7
- Ligands
- NAG, FUC
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-lymphocyte activation antigen CD80 | protein | 106 | 8% helix, 56% strand | P33681 |
| B, D | Programmed cell death 1 ligand 1 | protein | 209 | 6% helix, 55% strand | Q9NZQ7 |
| C | T-lymphocyte activation antigen CD80 | protein | 97 | 3% helix, 51% strand | P33681 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains B, D
- GOL · Glycerol · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.72 | 0.86 | 47 | GOL |
| 2 | 62 | 0.38 | 0.79 | 16 | empty |
| 3 | 108 | 0.36 | 0.74 | 18 | empty |
| 4 | 72 | 0.34 | 0.76 | 21 | empty |
| 5 | 57 | 0.27 | 0.74 | 16 | empty |
Interfaces
6 interfaces between chains.
- B–D · 748 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 571 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 566 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 42 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 39 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 glycan, 6 disulfide, 1 modified (N-glycosylation, disulfide, phosphorylation).
Compared structures
- 7TPS · Crystal structure of ALPN-202 (engineered CD80 vIgD) in complex with PD-L1 · the same entry in another collection · chain A against A, TM-score 1.00
- P33681 · AlphaFold monomer V2.0 prediction for T-lymphocyte activation antigen CD80 (P33681) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P33681
- Every structure of UniProt Q9NZQ7
- Elsewhere: RCSB PDB 7TPS · PDBe 7TPS · UniProt P33681 · UniProt Q9NZQ7
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