MolNFT v1 · #163185 · protein
Structure of properdin lacking TSR3 based on anomalous data
6RV6: “Structure of properdin lacking TSR3 based on anomalous data”. X-ray diffraction, 4 ligands (MAN, FUC, BGC), 3 pockets (best druggability 0.51). MolNFT v1 #163185 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6RV6
- Type
- protein
- Length
- 385 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Properdin
- UniProt
- P27918
- Ligands
- MAN, FUC, BGC, NAG
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Properdin | protein | 165 | 2% helix, 35% strand | P27918 |
| B | Properdin | protein | 220 | 5% helix, 35% strand | P27918 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.51 | 0.77 | 28 | empty |
| 2 | 221 | 0.50 | 0.76 | 25 | empty |
| 3 | 77 | 0.37 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1190 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 16 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 6RV6 · PDBe 6RV6 · UniProt P27918
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