MolNFT v1 · #49132 · protein
Crystal structure of the ribosome inactivating protein PDL4 from P. dioica leaves in complex with adenine
2QES · Ribosome-inactivating protein pd-L4: “Crystal structure of the ribosome inactivating protein PDL4 from P. dioica leaves in complex with adenine”. X-ray diffraction, 1 ligand (ADE), 1 pocket (best druggability 0.45). MolNFT v1 #49132…
- 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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