Research workbench
Ccdb dimer from V. fisheri in complex with one C-terminal domain of F- plasmid ccda
Analyse Ccdb dimer from V. fisheri in complex with one C-terminal domain of F- plasmid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TCJ
- Type
- protein
- Length
- 240 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ccdb; Protein ccda
- UniProt
- Q84B82, P62553
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ccdb | protein | 104 | 27% helix, 33% strand | Q84B82 |
| B | Ccdb | protein | 103 | 27% helix, 33% strand | Q84B82 |
| T | Protein ccda | protein | 33 | 79% helix, 0% strand | P62553 |
Ligands and binding sites
- ACT · Acetate ion · additive · chains A, B, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.31 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 921 Ų buried · 9 hydrogen bonds · protein-protein
- B–T · 832 Ų buried · 5 hydrogen bonds · protein-protein
- A–T · 630 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3TCJ · CcdB dimer from V. fisheri in complex with one C-terminal domain of F-plasmid CcdA · the same entry in another collection · chain A against A, TM-score 1.00
- P62553 · AlphaFold monomer V2.0 prediction for antitoxin ccda (P62553) · a predicted model of the same protein · chain T against A, TM-score 0.62
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 Q84B82
- Every structure of UniProt P62553
- Elsewhere: RCSB PDB 3TCJ · PDBe 3TCJ · UniProt Q84B82 · UniProt P62553
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