Research workbench
Crystal structure of a ribosome inactivating protein in its naturally inhibited form
Analyse Crystal structure of a ribosome inactivating protein in its naturally inhibited… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TFM
- Type
- protein
- Length
- 495 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Himalayan mistletoe ribosome-inactivating protein
- Ligands
- P6C, NAG, BMA, GAL, BGC
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Himalayan mistletoe ribosome-inactivating protein | protein | 240 | 38% helix, 25% strand | — |
| B | Himalayan mistletoe ribosome-inactivating protein | protein | 255 | 10% helix, 39% strand | — |
Ligands and binding sites
- P6C · 2-amino-4-isopropyl-pteridine-6-carboxylic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar · 3 copies
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains B
- BGC · beta-D-glucopyranose · sugar · chains 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 | 333 | 0.76 | 0.87 | 56 | empty |
| 2 | 150 | 0.59 | 0.83 | 22 | P6C |
| 3 | 176 | 0.52 | 0.78 | 26 | empty |
| 4 | 160 | 0.50 | 0.78 | 25 | empty |
| 5 | 65 | 0.44 | 0.82 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1333 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1TFM · Crystal structure of a ribosome inactivating protein in its naturally inhibited form · 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
- Elsewhere: RCSB PDB 1TFM · PDBe 1TFM
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