Research workbench
Crystal structure of human complement C3B in complex with smallpox inhibitor of complement (spice)
Analyse Crystal structure of human complement C3B in complex with smallpox inhibitor of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FOB
- Type
- protein
- Length
- 1,784 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3 beta chain; Complement C3B alpha' chain; Smallpox inhibitor of complement…
- UniProt
- P01024, Q76U65
- Ligands
- NAG, BMA, FUC, NA, IOD, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3 beta chain | protein | 642 | 7% helix, 50% strand | P01024 |
| B | Complement C3B alpha' chain | protein | 902 | 28% helix, 33% strand | P01024 |
| C | Smallpox inhibitor of complement spice, D15L | protein | 240 | 5% helix, 37% strand | Q76U65 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
- NA · Sodium ion · metal · 2 copies · chains A, B
- IOD · Iodide ion · ion · 7 copies · chains A, B, C
- CL · Chloride ion · ion · 5 copies · chains A, B, C
- GOL · Glycerol · additive · 24 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.83 | 0.86 | 92 | CL |
| 2 | 1198 | 0.77 | 0.79 | 104 | GOL |
| 3 | 51 | 0.67 | 0.96 | 24 | empty |
| 4 | 464 | 0.64 | 0.77 | 61 | GOL, IOD |
| 5 | 507 | 0.64 | 0.77 | 52 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5137 Ų buried · 68 hydrogen bonds · protein-protein
- B–C · 1409 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 526 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5FOB · Crystal Structure of Human Complement C3b in complex with Smallpox Inhibitor of… · the same entry in another collection · chain A against A, TM-score 1.00
- P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · 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 P01024
- Every structure of UniProt Q76U65
- Elsewhere: RCSB PDB 5FOB · PDBe 5FOB · UniProt P01024 · UniProt Q76U65
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