MolNFT v1 · #31692 · protein
Structure of mammalian C3 with an intact thioester at 3A resolution
2B39: “Structure of mammalian C3 with an intact thioester at 3A resolution”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.82). MolNFT v1 #31692 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2B39
- Type
- protein
- Length
- 3,220 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C3
- UniProt
- Q2UVX4
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | C3 | protein | 1610 | 19% helix, 32% strand | Q2UVX4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.82 | 0.87 | 82 | empty |
| 2 | 893 | 0.80 | 0.82 | 93 | empty |
| 3 | 939 | 0.80 | 0.81 | 89 | empty |
| 4 | 799 | 0.79 | 0.83 | 69 | empty |
| 5 | 258 | 0.79 | 0.91 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 1084 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- Q2UVX4 · AlphaFold monomer V2.0 prediction for complement C3 (Q2UVX4) · a predicted model of the same protein · chain B against A, TM-score 0.67
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 Q2UVX4
- Elsewhere: RCSB PDB 2B39 · PDBe 2B39 · UniProt Q2UVX4
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