Research workbench
Complement component-9
Analyse Complement component-9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CXO
- Type
- protein
- Length
- 914 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement component C9
- UniProt
- P06683
- Ligands
- NAG, BMA, ZN, CA, MG
- Pockets
- 17 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement component C9 | protein | 465 | 24% helix, 26% strand | P06683 |
| B | Complement component C9 | protein | 449 | 24% helix, 27% strand | P06683 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 5 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.64 | 0.77 | 58 | empty |
| 2 | 351 | 0.64 | 0.79 | 40 | empty |
| 3 | 108 | 0.64 | 0.88 | 27 | empty |
| 4 | 83 | 0.62 | 0.89 | 24 | empty |
| 5 | 90 | 0.61 | 0.89 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 162 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 4 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 P06683
- Elsewhere: RCSB PDB 6CXO · PDBe 6CXO · UniProt P06683
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