Research workbench
The structure of the complex between complement receptor CR2 and its ligand complement fragment C3D
Analyse The structure of the complex between complement receptor CR2 and its ligand… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OED
- Type
- protein
- Length
- 848 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3; Complement receptor type 2
- UniProt
- P01024, P20023
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Complement C3 | protein | 294 | 61% helix, 2% strand | P01024 |
| C, D | Complement receptor type 2 | protein | 130 | 0% helix, 41% strand | P20023 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.84 | 0.87 | 72 | empty |
| 2 | 856 | 0.84 | 0.86 | 62 | empty |
| 3 | 529 | 0.65 | 0.77 | 55 | empty |
| 4 | 232 | 0.60 | 0.80 | 29 | empty |
| 5 | 113 | 0.49 | 0.80 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1231 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1177 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 542 Ų buried · 2 hydrogen bonds · protein-protein
- C–B · 89 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 83 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3OED · The structure of the complex between complement receptor CR2 and its ligand complement… · the same entry in another collection · chain D against D, TM-score 1.00
- P20023 · AlphaFold monomer V2.0 prediction for complement receptor type 2 (P20023) · a predicted model of the same protein · chain C against A, TM-score 0.96
- P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain A 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 P01024
- Every structure of UniProt P20023
- Elsewhere: RCSB PDB 3OED · PDBe 3OED · UniProt P01024 · UniProt P20023
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