Research workbench
Crystal structure of ribosome inactivating protein from momordica balsamina with uracil at 1.70 ångström resolution
Analyse Crystal structure of ribosome inactivating protein from momordica balsamina… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ILX
- Type
- protein
- Length
- 246 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome inactivating protein
- EC
- 3.2.2.22
- UniProt
- D9J2T9
- Ligands
- URA, NAG
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosome inactivating protein (EC 3.2.2.22) | protein | 246 | 42% helix, 25% strand | D9J2T9 |
Ligands and binding sites
- URA · Uracil · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.52 | 0.81 | 18 | URA, EDO |
| 2 | 70 | 0.37 | 0.77 | 16 | empty |
Modifications
Observed in the structure: 1 glycan (N-glycosylation).
Compared structures
- 5ILX · Crystal structure of Ribosome inactivating protein from Momordica balsamina with Uracil… · the same entry in another collection · 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 D9J2T9
- Elsewhere: RCSB PDB 5ILX · PDBe 5ILX · UniProt D9J2T9
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