MolNFT v1 · #18295 · protein
Globular head of the complement system protein C1Q
1PK6 · Complement C1Q subcomponent, a chain precursor: “Globular head of the complement system protein C1Q”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.45). MolNFT v1 #18295 on GenesisL1: 3D structure, binding sites…
- PDB
- 1PK6
- Type
- protein
- Length
- 394 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C1Q subcomponent, a chain precursor; Complement C1Q subcomponent, B chain…
- UniProt
- P02745, P02746, P02747
- Ligands
- CA
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C1Q subcomponent, a chain precursor | protein | 133 | 0% helix, 57% strand | P02745 |
| B | Complement C1Q subcomponent, B chain precursor | protein | 132 | 0% helix, 60% strand | P02746 |
| C | Complement C1Q subcomponent, C chain precursor | protein | 129 | 0% helix, 55% strand | P02747 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.45 | 0.77 | 20 | empty |
| 2 | 70 | 0.34 | 0.76 | 15 | empty |
| 3 | 51 | 0.26 | 0.74 | 14 | empty |
| 4 | 54 | 0.26 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1044 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1014 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 949 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1PK6 · Globular Head of the Complement System Protein C1q · the same entry in another collection · chain A against A, 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 C 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 B 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 1PK6 · PDBe 1PK6 · UniProt P02745 · UniProt P02746 · UniProt P02747
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