Research workbench
E. COLI transcriptional regulator rutr with dihydrouracil
Analyse E. COLI transcriptional regulator rutr with dihydrouracil in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XK4
- Type
- protein
- Length
- 787 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional regulator rutr
- UniProt
- P0ACU2
- Ligands
- DUC
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Hth-type transcriptional regulator rutr | protein | 196 | 79% helix, 0% strand | P0ACU2 |
| C | Hth-type transcriptional regulator rutr | protein | 199 | 78% helix, 0% strand | P0ACU2 |
Ligands and binding sites
- DUC · Dihydropyrimidine-2,4(1H,3H)-dione · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.66 | 0.91 | 28 | empty |
| 2 | 318 | 0.57 | 0.76 | 36 | empty |
| 3 | 257 | 0.54 | 0.76 | 36 | empty |
| 4 | 227 | 0.50 | 0.75 | 35 | empty |
| 5 | 53 | 0.36 | 0.79 | 13 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2213 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 2194 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 747 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 85 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4XK4 · E. coli transcriptional regulator RUTR with dihydrouracil · the same entry in another collection · chain A against A, TM-score 1.00
- P0ACU2 · AlphaFold monomer V2.0 prediction for hth-type transcriptional regulator rutr (P0ACU2) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0ACU2
- Elsewhere: RCSB PDB 4XK4 · PDBe 4XK4 · UniProt P0ACU2
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