MolNFT v1 · #62559 · protein
Complex of ricin a chain and pyrimidine-based inhibitor
3EJ5: “Complex of ricin a chain and pyrimidine-based inhibitor”. X-ray diffraction, 1 ligand (EJ5), 3 pockets (best druggability 0.54). MolNFT v1 #62559 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3EJ5
- Type
- protein
- Length
- 257 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ricin a chain
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- EJ5
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Ricin a chain (EC 3.2.2.22) | protein | 257 | 42% helix, 23% strand | P02879 |
Ligands and binding sites
- EJ5 · 4-[3-(2-amino-4-hydroxy-6-oxo-1,6-dihydropyrimidin-5-yl)propyl]benzoic acid · ligand · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.54 | 0.79 | 31 | EJ5 |
| 2 | 56 | 0.35 | 0.78 | 12 | empty |
| 3 | 54 | 0.25 | 0.72 | 20 | empty |
Compared structures
- 3EJ5 · complex of Ricin A chain and pyrimidine-based inhibitor · the same entry in another collection · chain X against X, 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 P02879
- Elsewhere: RCSB PDB 3EJ5 · PDBe 3EJ5 · UniProt P02879
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