MolNFT v1 · #39637 · protein
Human complement component C3B
2I07 · Complement C3B: “Human complement component C3B”. X-ray diffraction, 2 ligands (NAG, MAN), 20 pockets (best druggability 0.75). MolNFT v1 #39637 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2I07
- Type
- protein
- Length
- 1,531 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3B
- UniProt
- P01024
- Ligands
- NAG, MAN
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3B | protein | 630 | 6% helix, 50% strand | P01024 |
| B | Complement C3B | protein | 901 | 23% helix, 31% strand | P01024 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- MAN · alpha-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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.75 | 0.78 | 78 | empty |
| 2 | 137 | 0.74 | 0.93 | 26 | empty |
| 3 | 435 | 0.72 | 0.83 | 45 | empty |
| 4 | 180 | 0.61 | 0.83 | 32 | empty |
| 5 | 156 | 0.61 | 0.84 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 5300 Ų buried · 72 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 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 2I07 · PDBe 2I07 · UniProt P01024
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