MolNFT v1 · #147574 · protein
Complement component C3B in complex with a nanobody
6EHG · Complement C3: “Complement component C3B in complex with a nanobody”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.79). MolNFT v1 #147574 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6EHG
- Type
- protein
- Length
- 1,665 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3; HC3NB1
- UniProt
- P01024
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3 | protein | 638 | 8% helix, 51% strand | P01024 |
| B | Complement C3 | protein | 903 | 25% helix, 32% strand | P01024 |
| C | HC3NB1 | protein | 124 | 7% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.79 | 0.80 | 93 | empty |
| 2 | 63 | 0.72 | 0.98 | 22 | empty |
| 3 | 439 | 0.71 | 0.82 | 46 | empty |
| 4 | 143 | 0.65 | 0.87 | 23 | empty |
| 5 | 503 | 0.63 | 0.76 | 42 | empty |
Interfaces
2 interfaces between chains.
- A–B · 5548 Ų buried · 79 hydrogen bonds · protein-protein
- B–C · 702 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 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 6EHG · PDBe 6EHG · UniProt P01024
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