Research workbench
Structure of a functional properdin monomer
Analyse Structure of a functional properdin monomer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RUS
- Type
- protein
- Length
- 454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Homo sapiens
- Molecule
- Properdin
- UniProt
- P27918
- Ligands
- MAN, FUC, BGC, NAG, SO4
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · resolution 2.8 · 2 distinct chains · 4% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Properdin | protein | 234 | 3% helix, 29% strand | P27918 |
| B | Properdin | protein | 220 | 4% helix, 33% strand | P27918 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 15 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 5 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- SO4 · Sulfate ion · ion · 2 copies · 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 | 0.44 | 0.77 | 21 | empty |
| 2 | 153 | 0.44 | 0.75 | 25 | empty |
| 3 | 104 | 0.34 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1140 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 20 glycan (disulfide, C-mannosylation, O-glycosylation, N-glycosylation).
Compared structures
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 P27918
- Elsewhere: RCSB PDB 6RUS · PDBe 6RUS · UniProt P27918
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