Research workbench
Crystal structure of human complement C3B in complex with CR1 (CCP15- 17)
Analyse Crystal structure of human complement C3B in complex with CR1 (CCP15- 17) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FO9
- Type
- protein
- Length
- 3,476 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3 beta chain; Complement C3B alpha' chain; Complement receptor type 1
- UniProt
- P01024, P17927
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Complement C3 beta chain | protein | 642 | 7% helix, 50% strand | P01024 |
| B, E | Complement C3B alpha' chain | protein | 903 | 25% helix, 33% strand | P01024 |
| C, F | Complement receptor type 1 | protein | 193 | 0% helix, 33% strand | P17927 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.77 | 0.79 | 88 | empty |
| 2 | 782 | 0.77 | 0.81 | 57 | empty |
| 3 | 816 | 0.76 | 0.80 | 84 | empty |
| 4 | 530 | 0.76 | 0.84 | 61 | empty |
| 5 | 701 | 0.75 | 0.81 | 55 | empty |
Interfaces
9 interfaces between chains.
- D–E · 5281 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 5260 Ų buried · 68 hydrogen bonds · protein-protein
- A–D · 1539 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1421 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1386 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5FO9 · Crystal Structure of Human Complement C3b in Complex with CR1 (CCP15- 17) · the same entry in another collection · chain F against F, TM-score 1.00
- P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P17927 · AlphaFold monomer V2.0 prediction for complement receptor type 1 (P17927) · a predicted model of the same protein · chain F against A, TM-score 0.88
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 P17927
- Elsewhere: RCSB PDB 5FO9 · PDBe 5FO9 · UniProt P01024 · UniProt P17927
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