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Structure of the complex of type 1 ribosome inactivating protein from Momordica balsamina with a nucleotide, cytidine monophosphate at 1.80 A resolution
Analyse Structure of the complex of type 1 ribosome inactivating protein from Momordica… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZU0
- Type
- protein
- Length
- 246 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Momordica balsamina
- Molecule
- Ribosome inactivating protein
- EC
- 3.2.2.22
- UniProt
- D9J2T9
- Ligands
- C5P, NAG
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosome inactivating protein (EC 3.2.2.22) | protein | 246 | 43% helix, 24% strand | D9J2T9 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- GOL · Glycerol · additive · 2 copies · 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 | 125 | 0.50 | 0.80 | 21 | C5P |
| 2 | 57 | 0.31 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 1 glycan (N-glycosylation).
Compared structures
- 4ZU0 · Structure of the complex of type 1 ribosome inactivating protein from momordica balsamina… · 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 4ZU0 · PDBe 4ZU0 · UniProt D9J2T9
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