Research workbench
Crystal structure of the laci family member, purr, bound to DNA: minor groove binding by alpha helices
Analyse Crystal structure of the laci family member, purr, bound to DNA: minor groove… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PUF
- 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'); Protein (purine…
- UniProt
- P0ACP7
- Ligands
- GUN
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 13% 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 | Protein (purine repressor) | protein | 338 | 45% helix, 13% strand | P0ACP7 |
Ligands and binding sites
- GUN · Guanine · 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 | 147 | 0.59 | 0.84 | 34 | GUN |
| 2 | 181 | 0.43 | 0.73 | 19 | empty |
| 3 | 177 | 0.42 | 0.73 | 28 | empty |
Interfaces
1 interface between chains.
- B–A · 521 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 2PUF · Crystal structure of the laci family member, purr, bound to DNA: minor groove binding by… · 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 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 2PUF · PDBe 2PUF · UniProt P0ACP7
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