Research workbench
Crystal structure of pd-1 in complex with tislelizumab Fab
Analyse Crystal structure of pd-1 in complex with tislelizumab Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BXA
- Type
- protein
- Length
- 1,053 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death protein 1; Heavy chain; Light chain
- UniProt
- Q15116
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Programmed cell death protein 1 | protein | 103 | 3% helix, 52% strand | Q15116 |
| B | Heavy chain | protein | 212 | 6% helix, 50% strand | — |
| C | Light chain | protein | 213 | 6% helix, 46% strand | — |
| P | Programmed cell death protein 1 | protein | 103 | 3% helix, 49% strand | Q15116 |
| H | Heavy chain | protein | 211 | 7% helix, 48% strand | — |
| L | Light chain | protein | 211 | 5% helix, 49% strand | — |
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 | 994 | 0.75 | 0.78 | 110 | empty |
| 2 | 785 | 0.68 | 0.75 | 65 | empty |
| 3 | 634 | 0.67 | 0.77 | 72 | empty |
| 4 | 77 | 0.53 | 0.86 | 25 | empty |
| 5 | 258 | 0.52 | 0.75 | 32 | empty |
Interfaces
10 interfaces between chains.
- B–C · 1843 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1839 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 635 Ų buried · 8 hydrogen bonds · protein-protein
- P–L · 573 Ų buried · 9 hydrogen bonds · protein-protein
- A–P · 506 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7BXA · Crystal structure of PD-1 in complex with tislelizumab Fab · the same entry in another collection · chain L against L, 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 A 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 Q15116
- Elsewhere: RCSB PDB 7BXA · PDBe 7BXA · UniProt Q15116
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