MolNFT v1 · #1822 · protein + DNA
Purine repressor mutant-hypoxanthine-palindromic operator complex
1BDH · DNA (5'- D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*…: “Purine repressor mutant-hypoxanthine-palindromic operator complex”. X-ray diffraction, 1 ligand (HPA), 3 pockets (best druggability 0.62). MolNFT v1 #1822 on GenesisL1…
- PDB
- 1BDH
- 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
- HPA
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% 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 | 46% 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 | 128 | 0.62 | 0.86 | 31 | HPA |
| 2 | 165 | 0.43 | 0.74 | 31 | empty |
| 3 | 147 | 0.38 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- B–A · 477 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 1BDH · Purine repressor mutant-hypoxanthine-palindromic operator complex · 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 1BDH · PDBe 1BDH · UniProt P0ACP7
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