MolNFT v1 · #41196 · protein
Crystallographic structure of human C1Q globular heads complexed to phosphatidyl-serine
2JG8 · Complement C1Q subcomponent subunit a: “Crystallographic structure of human C1Q globular heads complexed to phosphatidyl-serine”. X-ray diffraction, 3 ligands (SEP, NAG, CA), 10 pockets (best druggability 0.82). MolNFT v1 #41196 on…
- PDB
- 2JG8
- Type
- protein
- Length
- 791 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C1Q subcomponent subunit a; Complement C1Q subcomponent subunit B; Complement…
- UniProt
- P02745, P02746, P02747
- Ligands
- SEP, NAG, CA
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 0% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Complement C1Q subcomponent subunit a | protein | 133 | 0% helix, 56% strand | P02745 |
| B | Complement C1Q subcomponent subunit B | protein | 133 | 0% helix, 59% strand | P02746 |
| C | Complement C1Q subcomponent subunit C | protein | 131 | 2% helix, 54% strand | P02747 |
| E | Complement C1Q subcomponent subunit B | protein | 132 | 0% helix, 55% strand | P02746 |
| F | Complement C1Q subcomponent subunit C | protein | 129 | 0% helix, 56% strand | P02747 |
Ligands and binding sites
- SEP · Phosphoserine · ligand · chains C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.82 | 0.97 | 29 | empty |
| 2 | 356 | 0.66 | 0.81 | 49 | empty |
| 3 | 144 | 0.50 | 0.79 | 22 | empty |
| 4 | 137 | 0.48 | 0.78 | 21 | SEP |
| 5 | 101 | 0.46 | 0.80 | 19 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1071 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1059 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1045 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1019 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 963 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2JG8 · Crystallographic structure of human C1q globular heads complexed to phosphatidyl-serine · the same entry in another collection · chain D against D, TM-score 1.00
- P02747 · AlphaFold monomer V2.0 prediction for complement C1Q subcomponent subunit C (P02747) · a predicted model of the same protein · chain F against A, TM-score 1.00
- P02746 · AlphaFold monomer V2.0 prediction for complement C1Q subcomponent subunit B (P02746) · a predicted model of the same protein · chain E against A, TM-score 1.00
- P02745 · AlphaFold monomer V2.0 prediction for complement C1Q subcomponent subunit a (P02745) · a predicted model of the same protein · chain A 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 P02745
- Every structure of UniProt P02746
- Every structure of UniProt P02747
- Elsewhere: RCSB PDB 2JG8 · PDBe 2JG8 · UniProt P02745 · UniProt P02746 · UniProt P02747
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