Research workbench
Crystal structure of the DNA-binding domains of yvoa in complex with palindromic operator DNA
Analyse Crystal structure of the DNA-binding domains of yvoa in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U0Y
- Type
- protein + DNA
- Length
- 329 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional repressor yvoa; DNA (5'-D(P*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*A…
- UniProt
- O34817
- Ligands
- CL
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hth-type transcriptional repressor yvoa | protein | 75 | 48% helix, 12% strand | O34817 |
| D | Hth-type transcriptional repressor yvoa | protein | 74 | 47% helix, 12% strand | O34817 |
| E, F | DNA (5'-D(P*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*T)- 3') | dna | 15 | — | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B, E, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.70 | 0.82 | 28 | empty |
| 2 | 79 | 0.50 | 0.84 | 18 | empty |
| 3 | 152 | 0.48 | 0.78 | 16 | CL |
| 4 | 103 | 0.46 | 0.80 | 15 | CL |
| 5 | 151 | 0.46 | 0.77 | 24 | empty |
Interfaces
14 interfaces between chains.
- E–F · 628 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- D–E · 519 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–F · 514 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–E · 513 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–E · 492 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 4U0Y · Crystal structure of the DNA-binding domains of YvoA in complex with palindromic operator… · the same entry in another collection · chain F against F, TM-score 1.00
- O34817 · AlphaFold monomer V2.0 prediction for hth-type transcriptional repressor nagr (O34817) · a predicted model of the same protein · chain D 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 O34817
- Elsewhere: RCSB PDB 4U0Y · PDBe 4U0Y · UniProt O34817
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