Research workbench
Structure of a complement factor-receptor complex
Analyse Structure of a complement factor-receptor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AKK
- Type
- protein
- Length
- 3,006 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3 beta chain; Complement C3B alpha' chain; Integrin alpha-M
- UniProt
- P01024, P11215
- Ligands
- NAG, MAN, BMA, K, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C | Complement C3 beta chain | protein | 645 | 8% helix, 48% strand | P01024 |
| A | Complement C3B alpha' chain | protein | 842 | 23% helix, 25% strand | P01024 |
| D, H | Integrin alpha-M | protein | 185 | 38% helix, 21% strand | P11215 |
| E | Complement C3B alpha' chain | protein | 504 | 10% helix, 41% strand | P01024 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, C, E
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- K · Potassium ion · metal · 2 copies · chains B, A, C, E
- MG · Magnesium ion · metal · 2 copies · chains A, D, H
- GOL · Glycerol · additive · 3 copies · chains B, C, E
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 | 1076 | 0.85 | 0.86 | 120 | K |
| 2 | 755 | 0.82 | 0.86 | 81 | K |
| 3 | 725 | 0.82 | 0.86 | 84 | empty |
| 4 | 783 | 0.77 | 0.81 | 82 | empty |
| 5 | 1199 | 0.77 | 0.79 | 141 | GOL |
Interfaces
11 interfaces between chains.
- C–E · 4290 Ų buried · 64 hydrogen bonds · protein-protein
- B–A · 4149 Ų buried · 67 hydrogen bonds · protein-protein
- B–H · 864 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 861 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 851 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7AKK · Structure of a complement factor-receptor complex · the same entry in another collection · chain H against H, TM-score 1.00
- P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P11215 · AlphaFold monomer V2.0 prediction for integrin alpha-M (P11215) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 P11215
- Elsewhere: RCSB PDB 7AKK · PDBe 7AKK · UniProt P01024 · UniProt P11215
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