Research workbench
Crystal structure of bacillus thuringiensis plcr in complex with the peptide PAPR7 and DNA
Analyse Crystal structure of bacillus thuringiensis plcr in complex with the peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U3W
- Type
- protein + DNA
- Length
- 610 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional activator plcr protein; C-terminus heptapeptide from papr protein…
- UniProt
- Q45782, B7IR02
- Ligands
- CA
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transcriptional activator plcr protein | protein | 280 | 73% helix, 0% strand | Q45782 |
| P, Q | C-terminus heptapeptide from papr protein | protein | 7 | 0% helix, 0% strand | B7IR02 |
| Y | 5'-D(P*CP*TP*AP*TP*GP*CP*AP*AP*TP*AP*TP*TP*TP*CP*AP*TP*AP*T )-3' | dna | 18 | — | — |
| Z | 5'-D(P*AP*TP*AP*TP*GP*AP*AP*AP*TP*AP*TP*TP*GP*CP*AP*TP*AP*G )-3' | dna | 18 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, Z, B, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.76 | 0.83 | 60 | empty |
| 2 | 299 | 0.69 | 0.84 | 40 | empty |
| 3 | 233 | 0.66 | 0.84 | 33 | empty |
| 4 | 177 | 0.50 | 0.78 | 26 | empty |
| 5 | 113 | 0.40 | 0.76 | 20 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1966 Ų buried · 6 hydrogen bonds · protein-protein
- Y–Z · 791 Ų buried · 76 hydrogen bonds · nucleic-nucleic
- A–P · 759 Ų buried · 9 hydrogen bonds · protein-protein
- B–Q · 756 Ų buried · 9 hydrogen bonds · protein-protein
- B–Y · 380 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 3U3W · Crystal Structure of Bacillus thuringiensis PlcR in complex with the peptide PapR7 and DNA · the same entry in another collection · 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 Q45782
- Every structure of UniProt B7IR02
- Elsewhere: RCSB PDB 3U3W · PDBe 3U3W · UniProt Q45782 · UniProt B7IR02
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