MolNFT v1 · #163344 · protein
Crystal structure of properdin (tsr domains N1 & 456)
6S08: “Crystal structure of properdin (tsr domains N1 & 456)”. X-ray diffraction, 4 ligands (MAN, FUC, BGC), 2 pockets (best druggability 0.39). MolNFT v1 #163344 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6S08
- Type
- protein
- Length
- 311 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Properdin
- UniProt
- P27918
- Ligands
- MAN, FUC, BGC, NA
- Pockets
- 2 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Properdin | protein | 206 | 0% helix, 36% strand | P27918 |
| B | Properdin | protein | 105 | 4% helix, 50% strand | P27918 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · chains A, B
- NA · Sodium ion · metal · chains A
- PGE · Triethylene glycol · additive · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.39 | 0.75 | 27 | empty |
| 2 | 107 | 0.37 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1248 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 10 glycan (disulfide, C-mannosylation, O-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 6S08 · PDBe 6S08 · UniProt P27918
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.