MolNFT v1 · #163150 · protein
Human complement C3 in complex with the HC3NB1 nanobody
6RU5: “Human complement C3 in complex with the HC3NB1 nanobody”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.78). MolNFT v1 #163150 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6RU5
- Type
- protein
- Length
- 1,749 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3; HC3NB1
- UniProt
- P01024
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3 | protein | 643 | 5% helix, 46% strand | P01024 |
| B | Complement C3 | protein | 980 | 27% helix, 29% strand | P01024 |
| C | HC3NB1 | protein | 126 | 5% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B
- BMA · beta-D-mannopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 737 | 0.78 | 0.83 | 65 | empty |
| 2 | 887 | 0.76 | 0.79 | 74 | NAG |
| 3 | 82 | 0.71 | 0.95 | 23 | empty |
| 4 | 459 | 0.67 | 0.79 | 49 | empty |
| 5 | 436 | 0.66 | 0.79 | 43 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4990 Ų buried · 57 hydrogen bonds · protein-protein
- B–C · 506 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 257 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 P01024
- Elsewhere: RCSB PDB 6RU5 · PDBe 6RU5 · UniProt P01024
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