Research workbench
Crystal structure of type 1 ribosome inactivating protein from momordica balsamina with lipopolysaccharide at 1.6 ångström resolution
Analyse Crystal structure 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
- 4GUW
- Type
- protein
- Length
- 246 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RRNA N-glycosidase
- EC
- 3.2.2.22
- UniProt
- D9J2T9
- Ligands
- LP5, NAG
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RRNA N-glycosidase (EC 3.2.2.22) | protein | 246 | 42% helix, 22% strand | D9J2T9 |
Ligands and binding sites
- LP5 · (R)-((2R,3S,4R,5R,6R)-3-hydroxy-2-(hydroxymethyl)-5-((R)-3-hydroxytetradecanamido)-6-(phosphonooxy) tetrahydro-2H-pyran-4-yl) 3-hydroxytetradecanoate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.48 | 0.79 | 19 | LP5 |
| 2 | 58 | 0.32 | 0.76 | 13 | empty |
| 3 | 52 | 0.25 | 0.73 | 14 | empty |
Modifications
Observed in the structure: 1 glycan (N-glycosylation).
Compared structures
- 4GUW · Crystal structure of type 1 Ribosome inactivating protein from Momordica balsamina with… · 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 4GUW · PDBe 4GUW · UniProt D9J2T9
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