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
- 2PUB
- 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
- ADE
- Pockets
- 3 · best druggability 0.62
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
- ADE · Adenine · 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 | 149 | 0.62 | 0.84 | 33 | ADE |
| 2 | 181 | 0.44 | 0.74 | 31 | empty |
| 3 | 170 | 0.42 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 501 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 2PUB · Crystal structure of the laci family member, purr, bound to DNA: minor groove binding by… · the same entry in another collection · chain A against A, 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 2PUB · PDBe 2PUB · UniProt P0ACP7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.