Research workbench
Purine repressor-hypoxanthine-modified-purf-operator complex
Analyse Purine repressor-hypoxanthine-modified-purf-operator complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZAY
- Type
- protein + DNA
- Length
- 355 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*AP*CP*GP*AP*AP*AP*AP*TP*(1AP) P*TP*TP*TP*TP*CP*GP*T)-3'); Protein (purine…
- UniProt
- P0ACP7
- Ligands
- HPA
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | DNA (5'-D(*AP*AP*CP*GP*AP*AP*AP*AP*TP*(1AP) P*TP*TP*TP*TP*CP*GP*T)-3') | dna | 17 | — | — |
| A | Protein (purine repressor) | protein | 338 | 45% helix, 14% 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 | 132 | 0.63 | 0.86 | 30 | HPA |
| 2 | 207 | 0.44 | 0.73 | 17 | empty |
| 3 | 139 | 0.38 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- M–A · 521 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1ZAY · Purine repressor-hypoxanthine-modified-purf-operator complex · the same entry in another collection · chain M against M, 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 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 P0ACP7
- Elsewhere: RCSB PDB 1ZAY · PDBe 1ZAY · UniProt P0ACP7
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