Research workbench
Crystal structure of the complex of ribosome inactivating protein from momordica balsamina with peptidoglycan fragment at 1.78 a resolution
Analyse Crystal structure of the complex of ribosome inactivating protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LWX
- Type
- protein
- Length
- 248 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
- LAC, NAG, NDG
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RRNA N-glycosidase (EC 3.2.2.22) | protein | 248 | 42% helix, 25% strand | D9J2T9 |
Ligands and binding sites
- LAC · Lactic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- NDG · 2-acetamido-2-deoxy-alpha-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 | 140 | 0.55 | 0.81 | 20 | NDG, LAC |
| 2 | 51 | 0.31 | 0.76 | 13 | empty |
Modifications
Observed in the structure: 1 covalent, 1 glycan (covalent ligand, N-glycosylation).
Compared structures
- 4LWX · Crystal structure of the complex of Ribosome inactivating protein from Momordica… · 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 4LWX · PDBe 4LWX · UniProt D9J2T9
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