MolNFT v1 · #112069 · protein
Structural studies on a non-toxic homologue of type II rips from momordica charantia (bitter gourd)-native-2
4Z9W · RRNA N-glycosidase: “Structural studies on a non-toxic homologue of type II rips from momordica charantia (bitter gourd)-native-2”. X-ray diffraction, 3 ligands (NAG, FUC, BMA), 5 pockets (best druggability 0.65). MolNFT v1 #112069…
- PDB
- 4Z9W
- Type
- protein
- Length
- 508 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RRNA N-glycosidase
- EC
- 3.2.2.22
- UniProt
- B7X8M2
- Ligands
- NAG, FUC, BMA
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RRNA N-glycosidase (EC 3.2.2.22) | protein | 247 | 42% helix, 23% strand | B7X8M2 |
| B | RRNA N-glycosidase (EC 3.2.2.22) | protein | 261 | 13% helix, 38% strand | B7X8M2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, A
- FUC · alpha-L-fucopyranose · sugar
- BMA · beta-D-mannopyranose · sugar
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.65 | 0.89 | 27 | empty |
| 2 | 295 | 0.64 | 0.81 | 38 | EDO |
| 3 | 228 | 0.52 | 0.76 | 30 | empty |
| 4 | 145 | 0.46 | 0.77 | 19 | EDO |
| 5 | 67 | 0.37 | 0.78 | 27 | NAG |
Interfaces
1 interface between chains.
- A–B · 1798 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4Z9W · Structural studies on a non-toxic homologue of type II RIPs from Momordica charantia… · 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 B7X8M2
- Elsewhere: RCSB PDB 4Z9W · PDBe 4Z9W · UniProt B7X8M2
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