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Crystal structure of beta-luffin, a ribosome inactivating protein at 2.0A resolution
Analyse Crystal structure of beta-luffin, a ribosome inactivating protein at 2.0A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NIO
- Type
- protein
- Length
- 247 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B-luffin
- EC
- 3.2.2.22
- UniProt
- P22851
- Ligands
- NAG
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | B-luffin (EC 3.2.2.22) | protein | 247 | 40% helix, 25% strand | P22851 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 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 | 118 | 0.51 | 0.81 | 19 | empty |
| 2 | 75 | 0.33 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 3 glycan (N-glycosylation).
Compared structures
- 1NIO · Crystal structure of beta-luffin, a ribosome inactivating protein at 2.0A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P22851 · AlphaFold monomer V2.0 prediction for ribosome-inactivating protein luffin-B (P22851) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P22851
- Elsewhere: RCSB PDB 1NIO · PDBe 1NIO · UniProt P22851
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