Research workbench
CR2-C3D complex structure
Analyse CR2-C3D complex structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GHQ
- Type
- protein
- Length
- 570 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3; CR2/CD121/C3D/EPSTEIN-barr virus receptor
- UniProt
- P01024, P20023
- Ligands
- NDG, ZN
- Pockets
- 9 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3 | protein | 307 | 62% helix, 3% strand | P01024 |
| B | CR2/CD121/C3D/EPSTEIN-barr virus receptor | protein | 129 | 0% helix, 40% strand | P20023 |
| C | CR2/CD121/C3D/EPSTEIN-barr virus receptor | protein | 134 | 0% helix, 42% strand | P20023 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains B, A, C
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.59 | 0.76 | 39 | empty |
| 2 | 72 | 0.54 | 0.86 | 14 | empty |
| 3 | 126 | 0.43 | 0.76 | 20 | empty |
| 4 | 107 | 0.43 | 0.78 | 23 | empty |
| 5 | 165 | 0.42 | 0.74 | 23 | empty |
Interfaces
3 interfaces between chains.
- B–C · 544 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 432 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 222 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 1GHQ · CR2-C3D complex structure · the same entry in another collection · chain A against A, TM-score 1.00
- P20023 · AlphaFold monomer V2.0 prediction for complement receptor type 2 (P20023) · a predicted model of the same protein · chain B against A, TM-score 0.95
- P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P20023
- Elsewhere: RCSB PDB 1GHQ · PDBe 1GHQ · UniProt P01024 · UniProt P20023
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