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Crystal structure of the ribosome inactivating protein PDL4 from P. dioica leaves in complex with adenine
Analyse Crystal structure of the ribosome inactivating protein PDL4 from P. dioica… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QES
- Type
- protein
- Length
- 261 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome-inactivating protein pd-L4
- EC
- 3.2.2.22
- UniProt
- P84854
- Ligands
- ADE
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosome-inactivating protein pd-L4 (EC 3.2.2.22) | protein | 261 | 39% helix, 23% strand | P84854 |
Ligands and binding sites
- ADE · Adenine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.45 | 0.82 | 18 | ADE |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2QES · Crystal structure of the ribosome inactivating protein PDL4 from P. dioica leaves in… · the same entry in another collection · chain A against A, TM-score 1.00
- P84854 · AlphaFold monomer V2.0 prediction for ribosome-inactivating protein pd-L3/PD-L4 (P84854) · a predicted model of the same protein · chain A against A, 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 P84854
- Elsewhere: RCSB PDB 2QES · PDBe 2QES · UniProt P84854
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