Research workbench
Decay accelerating factor (CD55): the structure of an intact human complement regulator.
Analyse Decay accelerating factor (CD55): the structure of an intact human complement… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OK2
- Type
- protein
- Length
- 507 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement decay-accelerating factor
- UniProt
- P08174
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement decay-accelerating factor | protein | 254 | 1% helix, 42% strand | P08174 |
| B | Complement decay-accelerating factor | protein | 253 | 1% helix, 43% strand | P08174 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.52 | 0.75 | 48 | GOL |
| 2 | 113 | 0.41 | 0.76 | 20 | GOL |
Interfaces
1 interface between chains.
- A–B · 1026 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 1OK2 · Decay accelerating factor (CD55): the structure of an intact human complement regulator. · the same entry in another collection · chain A against A, TM-score 1.00
- P08174 · AlphaFold monomer V2.0 prediction for complement decay-accelerating factor (P08174) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P08174
- Elsewhere: RCSB PDB 1OK2 · PDBe 1OK2 · UniProt P08174
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