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
- 1OJY
- Type
- protein
- Length
- 1,011 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement decay-accelerating factor
- UniProt
- P08174
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 1% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement decay-accelerating factor | protein | 252 | 1% helix, 42% strand | P08174 |
| B, D | Complement decay-accelerating factor | protein | 253 | 1% helix, 42% strand | P08174 |
| C | Complement decay-accelerating factor | protein | 253 | 0% helix, 41% strand | P08174 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, B, D
- GOL · Glycerol · additive · 6 copies · chains B, D, A, C
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.56 | 0.76 | 49 | GOL |
| 2 | 244 | 0.48 | 0.74 | 44 | GOL |
| 3 | 230 | 0.48 | 0.74 | 43 | GOL |
| 4 | 70 | 0.42 | 0.81 | 22 | SO4 |
| 5 | 68 | 0.33 | 0.76 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1014 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 965 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 116 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 72 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 32 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 1OJY · Decay accelerating factor (cd55): the structure of an intact human complement regulator. · the same entry in another collection · chain D against D, TM-score 1.00
- P08174 · AlphaFold monomer V2.0 prediction for complement decay-accelerating factor (P08174) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 1OJY · PDBe 1OJY · UniProt P08174
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