Research workbench
Crystallographic structure of human C1Q globular heads (P1)
Analyse Crystallographic structure of human C1Q globular heads (P1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JG9
- Type
- protein
- Length
- 788 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
- CA
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Complement C1Q subcomponent subunit a | protein | 133 | 0% helix, 56% strand | P02745 |
| B, E | Complement C1Q subcomponent subunit B | protein | 132 | 0% helix, 58% strand | P02746 |
| C, F | Complement C1Q subcomponent subunit C | protein | 129 | 0% helix, 55% strand | P02747 |
Ligands and binding sites
- 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
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.81 | 0.96 | 27 | empty |
| 2 | 545 | 0.75 | 0.83 | 78 | empty |
| 3 | 71 | 0.48 | 0.84 | 19 | empty |
| 4 | 79 | 0.44 | 0.81 | 24 | empty |
| 5 | 72 | 0.40 | 0.79 | 17 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1008 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1007 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 998 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 989 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 950 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2JG9 · Crystallographic structure of human C1q globular heads (P1) · the same entry in another collection · chain F against F, 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 0.99
- 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 0.99
- 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 0.99
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 2JG9 · PDBe 2JG9 · UniProt P02745 · UniProt P02746 · UniProt P02747
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