MolNFT v1 · #163346 · protein
Crystal structure of properdin (tsr domains N12 & 456)
6S0A: “Crystal structure of properdin (tsr domains N12 & 456)”. X-ray diffraction, 4 ligands (MAN, FUC, BGC), 2 pockets (best druggability 0.36). MolNFT v1 #163346 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6S0A
- Type
- protein
- Length
- 368 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
- 2 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Properdin | protein | 208 | 0% helix, 38% strand | P27918 |
| B | Properdin | protein | 160 | 3% helix, 33% strand | P27918 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · 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 | 106 | 0.36 | 0.74 | 24 | empty |
| 2 | 74 | 0.34 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1294 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 14 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 6S0A · PDBe 6S0A · UniProt P27918
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