Research workbench
Crig bound to C3B
Analyse Crig bound to C3B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ICF
- Type
- protein
- Length
- 1,664 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3 beta chain; Complement C3 alpha chain; V-set and immunoglobulin…
- UniProt
- P01024, Q9Y279
- Ligands
- NAG, BMA, CA
- Pockets
- 19 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3 beta chain | protein | 642 | 7% helix, 46% strand | P01024 |
| B | Complement C3 alpha chain | protein | 903 | 23% helix, 29% strand | P01024 |
| S | V-set and immunoglobulin domain-containing protein 4 | protein | 119 | 3% helix, 43% strand | Q9Y279 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.85 | 0.87 | 111 | empty |
| 2 | 748 | 0.74 | 0.79 | 46 | empty |
| 3 | 436 | 0.70 | 0.81 | 44 | empty |
| 4 | 436 | 0.69 | 0.80 | 64 | empty |
| 5 | 219 | 0.66 | 0.84 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5063 Ų buried · 61 hydrogen bonds · protein-protein
- A–S · 1379 Ų buried · 10 hydrogen bonds · protein-protein
- B–S · 344 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2ICF · CRIg bound to C3b · 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
- Q9Y279 · AlphaFold monomer V2.0 prediction for V-set and immunoglobulin domain-containing protein… · a predicted model of the same protein · chain S 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 Q9Y279
- Elsewhere: RCSB PDB 2ICF · PDBe 2ICF · UniProt P01024 · UniProt Q9Y279
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