MolNFT v1 · #64594 · protein
Ccdb dimer in complex with two C-terminal ccda domains
3G7Z · Cytotoxic protein ccdb: “Ccdb dimer in complex with two C-terminal ccda domains”. X-ray diffraction, 2 pockets (best druggability 0.52). MolNFT v1 #64594 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3G7Z
- Type
- protein
- Length
- 269 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytotoxic protein ccdb; Protein ccda
- UniProt
- P62554, P62552
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytotoxic protein ccdb | protein | 101 | 25% helix, 38% strand | P62554 |
| C | Protein ccda | protein | 34 | 65% helix, 12% strand | P62552 |
| D | Protein ccda | protein | 33 | 82% helix, 6% strand | P62552 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.52 | 0.89 | 20 | empty |
| 2 | 55 | 0.49 | 0.86 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 967 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 945 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 853 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 635 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 592 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3G7Z · CcdB dimer in complex with two C-terminal CcdA domains · the same entry in another collection · chain D against D, TM-score 1.00
- P62554 · AlphaFold monomer V2.0 prediction for toxin ccdb (P62554) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P62552 · AlphaFold monomer V2.0 prediction for antitoxin ccda (P62552) · a predicted model of the same protein · chain C against A, TM-score 0.70
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 P62554
- Every structure of UniProt P62552
- Elsewhere: RCSB PDB 3G7Z · PDBe 3G7Z · UniProt P62554 · UniProt P62552
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