Research workbench
Crystal structure of properdin in complex with the ctc domain of C3/C3B
Analyse Crystal structure of properdin in complex with the ctc domain of C3/C3B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S0B
- Type
- protein
- Length
- 461 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Properdin; Complement C3
- UniProt
- P27918, P01024
- Ligands
- MAN, FUC, BGC, NAG
- Pockets
- 5 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Properdin | protein | 219 | 0% helix, 36% strand | P27918 |
| B | Properdin | protein | 103 | 4% helix, 46% strand | P27918 |
| C | Complement C3 | protein | 139 | 27% helix, 32% strand | P01024 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains A
- BGC · beta-D-glucopyranose · sugar · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.50 | 0.79 | 23 | empty |
| 2 | 123 | 0.47 | 0.79 | 21 | empty |
| 3 | 110 | 0.38 | 0.75 | 19 | empty |
| 4 | 114 | 0.37 | 0.74 | 22 | empty |
| 5 | 103 | 0.34 | 0.73 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1134 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1107 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 10 glycan (disulfide, C-mannosylation, N-glycosylation, O-glycosylation).
Compared structures
- 6S0B · Crystal Structure of Properdin in complex with the CTC domain of C3/C3b · the same entry in another collection · chain A against A, TM-score 1.00
- P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P27918 · AlphaFold monomer V2.0 prediction for properdin (P27918) · a predicted model of the same protein · chain B against A, TM-score 0.90
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
- Every structure of UniProt P01024
- Elsewhere: RCSB PDB 6S0B · PDBe 6S0B · UniProt P27918 · UniProt P01024
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