MolNFT v1 · #162951 · protein
Crystal structure of the C-terminal dimerization domain of the essential repressor ddro from radiation-resistant deinococcus bacteria (deinococcus deserti)
6RO6 · Hth-type transcriptional regulator ddroc: “Crystal structure of the C-terminal dimerization domain of the essential repressor ddro from…”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.69). MolNFT v1 #162951 on…
- PDB
- 6RO6
- Type
- protein
- Length
- 444 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional regulator ddroc
- UniProt
- C1CYP4
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 57% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hth-type transcriptional regulator ddroc | protein | 57 | 58% helix, 4% strand | C1CYP4 |
| C, D | Hth-type transcriptional regulator ddroc | protein | 56 | 55% helix, 4% strand | C1CYP4 |
| E | Hth-type transcriptional regulator ddroc | protein | 55 | 58% helix, 4% strand | C1CYP4 |
| F | Hth-type transcriptional regulator ddroc | protein | 53 | 60% helix, 4% strand | C1CYP4 |
| G, H | Hth-type transcriptional regulator ddroc | protein | 55 | 55% helix, 4% strand | C1CYP4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, C, B, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 696 | 0.69 | 0.77 | 62 | empty |
| 2 | 57 | 0.29 | 0.75 | 15 | SO4 |
Interfaces
12 interfaces between chains.
- A–C · 1065 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 975 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 625 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 558 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 556 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6RO6 · Crystal structure of the C-terminal dimerization domain of the essential repressor DdrO… · the same entry in another collection · chain H against H, TM-score 1.00
- C1CYP4 · AlphaFold monomer V2.0 prediction for hth-type transcriptional regulator ddroc (C1CYP4) · a predicted model of the same protein · chain F against A, TM-score 0.91
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 C1CYP4
- Elsewhere: RCSB PDB 6RO6 · PDBe 6RO6 · UniProt C1CYP4
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