Research workbench
Pcpr inducer binding domain complex with pentachlorophenol
Analyse Pcpr inducer binding domain complex with pentachlorophenol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RPN
- Type
- protein
- Length
- 873 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pcp degradation transcriptional activation protein
- UniProt
- P52679
- Ligands
- PCI
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Pcp degradation transcriptional activation protein | protein | 218 | 36% helix, 25% strand | P52679 |
| C | Pcp degradation transcriptional activation protein | protein | 217 | 36% helix, 25% strand | P52679 |
| A, B | Pcp degradation transcriptional activation protein | protein | 219 | 38% helix, 26% strand | P52679 |
Ligands and binding sites
- PCI · Pentachlorophenol · ligand · 8 copies · chains D, C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.78 | 0.98 | 21 | PCI |
| 2 | 101 | 0.78 | 0.97 | 21 | PCI |
| 3 | 91 | 0.77 | 0.97 | 23 | PCI |
| 4 | 93 | 0.76 | 0.97 | 21 | PCI |
| 5 | 124 | 0.57 | 0.84 | 21 | PCI |
Interfaces
4 interfaces between chains.
- A–B · 2068 Ų buried · 34 hydrogen bonds · protein-protein
- D–C · 2063 Ų buried · 42 hydrogen bonds · protein-protein
- D–B · 487 Ų buried · 12 hydrogen bonds · protein-protein
- D–A · 27 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4RPN · PcpR inducer binding domain complex with pentachlorophenol · the same entry in another collection · chain D against D, TM-score 1.00
- P52679 · AlphaFold monomer V2.0 prediction for pcp degradation transcriptional activation protein… · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P52679
- Elsewhere: RCSB PDB 4RPN · PDBe 4RPN · UniProt P52679
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