Research workbench
Crystal structure of the multidrug binding transcriptional repressor qacr bound to pentamadine
Analyse Crystal structure of the multidrug binding transcriptional repressor qacr bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RKW
- Type
- protein
- Length
- 744 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator qacr
- UniProt
- P0A0N4
- Ligands
- PNT, SO4
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, A, E | Transcriptional regulator qacr | protein | 186 | 74% helix, 0% strand | P0A0N4 |
Ligands and binding sites
- PNT · 1,5-bis(4-amidinophenoxy)pentane · ligand · chains A
- SO4 · Sulfate ion · ion · 22 copies · chains B, D, E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.84 | 0.89 | 45 | PNT |
| 2 | 760 | 0.75 | 0.80 | 68 | SO4 |
| 3 | 153 | 0.69 | 0.89 | 33 | empty |
| 4 | 141 | 0.55 | 0.82 | 24 | empty |
| 5 | 186 | 0.52 | 0.78 | 24 | SO4 |
Interfaces
3 interfaces between chains.
- D–E · 1641 Ų buried · 14 hydrogen bonds · protein-protein
- B–A · 1636 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 439 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1RKW · Crystal structure of the multidrug binding transcriptional repressor qacr bound to… · the same entry in another collection · chain B against B, TM-score 1.00
- P0A0N4 · AlphaFold monomer V2.0 prediction for hth-type transcriptional regulator qacr (P0A0N4) · a predicted model of the same protein · chain B 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 P0A0N4
- Elsewhere: RCSB PDB 1RKW · PDBe 1RKW · UniProt P0A0N4
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