Research workbench
Crystal structure of pd-L1 from P. dioica in complex with adenine
Analyse Crystal structure of pd-L1 from P. dioica in complex with adenine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LE7
- Type
- protein
- Length
- 522 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome-inactivating protein pd-L1/PD-L2
- EC
- 3.2.2.22
- UniProt
- P84853
- Ligands
- ADE, NAG
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribosome-inactivating protein pd-L1/PD-L2 (EC 3.2.2.22) | protein | 261 | 39% helix, 24% strand | P84853 |
Ligands and binding sites
- ADE · Adenine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.57 | 0.74 | 44 | empty |
Interfaces
1 interface between chains.
- A–B · 334 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3LE7 · Crystal structure of PD-L1 from P. dioica in complex with adenine · the same entry in another collection · chain A against A, TM-score 1.00
- P84853 · AlphaFold monomer V2.0 prediction for ribosome-inactivating protein pd-L1/PD-L2 (P84853) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P84853
- Elsewhere: RCSB PDB 3LE7 · PDBe 3LE7 · UniProt P84853
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.