Research workbench
Globular head of C1Q in complex with the nanobody C1QNB75
Analyse Globular head of C1Q in complex with the nanobody C1QNB75 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z6V
- Type
- protein
- Length
- 1,036 residues
- Chains
- 8
- 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
- NAG
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · 7 distinct chains · 2% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C1Q subcomponent subunit a | protein | 133 | 0% helix, 59% strand | P02745 |
| B, E | Complement C1Q subcomponent subunit B | protein | 133 | 0% helix, 59% strand | P02746 |
| C | Complement C1Q subcomponent subunit C | protein | 128 | 0% helix, 53% strand | P02747 |
| D | Complement C1Q subcomponent subunit a | protein | 133 | 0% helix, 51% strand | P02745 |
| F | Complement C1Q subcomponent subunit C | protein | 131 | 2% helix, 53% strand | P02747 |
| G | Nanobody C1Q75 | protein | 122 | 5% helix, 48% strand | — |
| H | Nanobody C1Q75 | protein | 123 | 5% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.64 | 0.75 | 61 | empty |
| 2 | 100 | 0.53 | 0.84 | 24 | empty |
| 3 | 195 | 0.50 | 0.77 | 27 | empty |
| 4 | 140 | 0.44 | 0.76 | 20 | empty |
| 5 | 61 | 0.36 | 0.79 | 13 | empty |
Interfaces
12 interfaces between chains.
- D–E · 1083 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1041 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 1038 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1006 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 985 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6Z6V · Globular head of C1q in complex with the nanobody C1qNb75 · the same entry in another collection · chain H against H, 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 C 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 0.98
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 6Z6V · PDBe 6Z6V · UniProt P02745 · UniProt P02746 · UniProt P02747
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.