Research workbench
Structural recognition and functional activation of fcrr by innate pentraxins
Analyse Structural recognition and functional activation of fcrr by innate pentraxins in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D5O
- Type
- protein
- Length
- 1,191 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serum amyloid P-component; Low affinity immunoglobulin gamma Fc region receptor II-a
- UniProt
- P02743, P12318
- Ligands
- NAG, SO4
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Serum amyloid P-component | protein | 204 | 5% helix, 44% strand | P02743 |
| F | Low affinity immunoglobulin gamma Fc region receptor II-a | protein | 171 | 4% helix, 48% strand | P12318 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 16 copies · chains A, E, B, C, D, F
- GOL · Glycerol · additive · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 905 | 0.73 | 0.77 | 86 | GOL |
| 2 | 78 | 0.66 | 0.92 | 27 | empty |
| 3 | 509 | 0.65 | 0.77 | 42 | empty |
| 4 | 346 | 0.59 | 0.76 | 46 | empty |
| 5 | 103 | 0.52 | 0.83 | 17 | empty |
Interfaces
7 interfaces between chains.
- A–B · 803 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 785 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 758 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 566 Ų buried · 2 hydrogen bonds · protein-protein
- C–F · 528 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 7 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 3D5O · Structural recognition and functional activation of FcrR by innate pentraxins · the same entry in another collection · chain F against F, TM-score 1.00
- P02743 · AlphaFold monomer V2.0 prediction for serum amyloid P-component (P02743) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P12318 · AlphaFold monomer V2.0 prediction for low affinity immunoglobulin gamma Fc region… · a predicted model of the same protein · chain F against A, TM-score 0.95
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 P02743
- Every structure of UniProt P12318
- Elsewhere: RCSB PDB 3D5O · PDBe 3D5O · UniProt P02743 · UniProt P12318
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