Research workbench
Crystal structure of full length yvoa in complex with palindromic operator DNA
Analyse Crystal structure of full length yvoa in complex with palindromic operator DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WWC
- Type
- protein + DNA
- Length
- 482 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional repressor yvoa; DNA (5'…
- UniProt
- O34817
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional repressor yvoa | protein | 213 | 24% helix, 34% strand | O34817 |
| B | Hth-type transcriptional repressor yvoa | protein | 231 | 25% helix, 32% strand | O34817 |
| E, F | DNA (5'- D(P*CP*AP*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*TP*GP*G)-3') | dna | 19 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.78 | 0.81 | 92 | EDO |
| 2 | 424 | 0.75 | 0.85 | 35 | EDO |
| 3 | 164 | 0.41 | 0.74 | 23 | EDO |
| 4 | 141 | 0.41 | 0.75 | 20 | EDO |
| 5 | 93 | 0.37 | 0.76 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1763 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 841 Ų buried · 76 hydrogen bonds · nucleic-nucleic
- A–E · 528 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–F · 527 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–E · 508 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 4WWC · Crystal structure of full length YvoA in complex with palindromic operator DNA · the same entry in another collection · chain A against A, 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 B 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 O34817
- Elsewhere: RCSB PDB 4WWC · PDBe 4WWC · UniProt O34817
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