Research workbench
Complex between C1Q globular heads and heparan sulfate
Analyse Complex between C1Q globular heads and heparan sulfate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WNU
- 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
- IDU, SGN, NAG
- Pockets
- 10 · 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, 57% 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
- IDU · 2-O-sulfo-beta-L-altropyranuronic acid · ligand · chains F
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · chains F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.81 | 0.96 | 30 | empty |
| 2 | 356 | 0.69 | 0.82 | 48 | empty |
| 3 | 84 | 0.53 | 0.85 | 20 | empty |
| 4 | 63 | 0.51 | 0.87 | 18 | empty |
| 5 | 164 | 0.49 | 0.77 | 23 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1051 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1030 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1013 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1003 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 951 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2WNU · Complex between c1q globular heads and heparan sulfate · the same entry in another collection · chain F against F, 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 E 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 2WNU · PDBe 2WNU · UniProt P02745 · UniProt P02746 · UniProt P02747
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