Research workbench
Crystal structure of nicotiana alata gemetophytic self-incompatibility associated SF11-RNase
Analyse Crystal structure of nicotiana alata gemetophytic self-incompatibility… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IOO
- Type
- protein
- Length
- 392 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SF11-RNase
- UniProt
- Q7SID5
- Ligands
- NAG, MAN, BMA, XYP
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SF11-RNase | protein | 196 | 35% helix, 19% strand | Q7SID5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- XYP · beta-D-xylopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.77 | 0.79 | 94 | empty |
Interfaces
1 interface between chains.
- A–B · 733 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1IOO · Crystal structure of nicotiana alata gemetophytic self-incompatibility associated… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7SID5 · AlphaFold monomer V2.0 prediction for ribonuclease S-F11 (Q7SID5) · 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 Q7SID5
- Elsewhere: RCSB PDB 1IOO · PDBe 1IOO · UniProt Q7SID5
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