MolNFT v1 · #115741 · protein
Structure of the complex of type 1 ribosome inactivating protein from momordica balsamina with a nucleoside, cytidine at 1.78 a resolution
5CSO: “Structure of the complex of type 1 ribosome inactivating protein from momordica balsamina with a nucleoside…”. X-ray diffraction, 2 ligands (CTN, NAG), 2 pockets (best druggability 0.51). MolNFT v1 #115741 on GenesisL1: 3D…
- PDB
- 5CSO
- 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
- CTN, NAG
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosome inactivating protein (EC 3.2.2.22) | protein | 246 | 42% helix, 24% strand | D9J2T9 |
Ligands and binding sites
- CTN · 4-amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone · 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 | 129 | 0.51 | 0.80 | 21 | CTN |
| 2 | 68 | 0.34 | 0.76 | 15 | empty |
Modifications
Observed in the structure: 1 glycan (N-glycosylation).
Compared structures
- 5CSO · 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 5CSO · PDBe 5CSO · UniProt D9J2T9
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