MolNFT v1 · #109225 · protein + DNA
Crystal structure of full length yvoa in complex with palindromic operator DNA
4WWC · Hth-type transcriptional repressor yvoa: “Crystal structure of full length yvoa in complex with palindromic operator DNA”. X-ray diffraction, 11 pockets (best druggability 0.78). MolNFT v1 #109225 on GenesisL1: 3D structure, binding…
- 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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