Research workbench
Structural studies on a non-toxic homologue of type II rips from momordica charantia (bitter gourd) in complex with N-acetyl D galactosamine
Analyse Structural studies on a non-toxic homologue of type II rips from momordica… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZFU
- 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, BMA, XYP, FUC, A2G
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RRNA N-glycosidase (EC 3.2.2.22) | protein | 247 | 44% helix, 24% strand | B7X8M2 |
| B | RRNA N-glycosidase (EC 3.2.2.22) | protein | 261 | 13% helix, 39% strand | B7X8M2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar
- XYP · beta-D-xylopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains B
- GOL · Glycerol · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.63 | 0.88 | 26 | empty |
| 2 | 303 | 0.61 | 0.79 | 37 | empty |
| 3 | 221 | 0.54 | 0.78 | 31 | empty |
| 4 | 134 | 0.45 | 0.77 | 19 | PGE |
Interfaces
1 interface between chains.
- A–B · 1802 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4ZFU · 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 4ZFU · PDBe 4ZFU · UniProt B7X8M2
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