Research workbench
Crig bound to C3C
Analyse Crig bound to C3C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ICE
- Type
- protein
- Length
- 2,468 residues
- Chains
- 8
- 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, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3 beta chain | protein | 642 | 7% helix, 50% strand | P01024 |
| B, E | Complement C3 alpha chain | protein | 183 | 2% helix, 57% strand | P01024 |
| C, F | Complement C3 alpha chain | protein | 296 | 16% helix, 37% strand | P01024 |
| S, T | V-set and immunoglobulin domain-containing protein 4 | protein | 119 | 5% helix, 52% strand | Q9Y279 |
| D | Complement C3 beta chain | protein | 630 | 6% helix, 49% strand | P01024 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.86 | 0.87 | 127 | empty |
| 2 | 563 | 0.81 | 0.87 | 67 | empty |
| 3 | 417 | 0.79 | 0.87 | 74 | empty |
| 4 | 108 | 0.75 | 0.95 | 29 | empty |
| 5 | 106 | 0.74 | 0.95 | 29 | empty |
Interfaces
11 interfaces between chains.
- D–E · 3577 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 3512 Ų buried · 60 hydrogen bonds · protein-protein
- D–T · 1230 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1219 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1161 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2ICE · CRIg bound to C3c · the same entry in another collection · chain T against T, 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 0.97
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 2ICE · PDBe 2ICE · UniProt P01024 · UniProt Q9Y279
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