Research workbench
Structure of the purr mutant, L54M, bound to hypoxanthine and purf operator DNA
Analyse Structure of the purr mutant, L54M, bound to hypoxanthine and purf operator DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VPW
- Type
- protein + DNA
- Length
- 355 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T )-3'); Purine repressor
- UniProt
- P0ACP7
- Ligands
- HPA
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'- D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T )-3') | dna | 17 | — | — |
| A | Purine repressor | protein | 338 | 45% helix, 15% strand | P0ACP7 |
Ligands and binding sites
- HPA · Hypoxanthine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.63 | 0.87 | 30 | HPA |
| 2 | 187 | 0.43 | 0.73 | 30 | empty |
| 3 | 168 | 0.42 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 512 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 1VPW · Structure of the purr mutant, L54M, bound to hypoxanthine and purf operator DNA · the same entry in another collection · chain B against B, TM-score 1.00
- P0ACP7 · AlphaFold monomer V2.0 prediction for hth-type transcriptional repressor purr (P0ACP7) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P0ACP7
- Elsewhere: RCSB PDB 1VPW · PDBe 1VPW · UniProt P0ACP7
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