Research workbench
The complex between phage 434 repression DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites
Analyse The complex between phage 434 repression DNA-binding domain and operator site… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PER
- Type
- protein + DNA
- Length
- 166 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*AP*AP*GP*TP*AP*CP*AP*GP*TP*TP*TP*TP*TP*CP*TP*TP*G P*TP*AP*T)-3'); DNA (5'…
- UniProt
- P16117
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'- D(*AP*AP*GP*TP*AP*CP*AP*GP*TP*TP*TP*TP*TP*CP*TP*TP*G P*TP*AP*T)-3') | dna | 20 | — | — |
| B | DNA (5'- D(*TP*AP*TP*AP*CP*AP*AP*GP*AP*AP*AP*AP*AP*CP*TP*GP*T P*AP*CP*T)-3') | dna | 20 | — | — |
| L, R | Protein (434 repressor) | protein | 63 | 63% helix, 0% strand | P16117 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.56 | 0.85 | 28 | empty |
| 2 | 60 | 0.31 | 0.76 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 861 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- A–L · 451 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–L · 441 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–R · 376 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–R · 374 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 1PER · The complex between phage 434 repression DNA-binding domain and operator site OR3… · 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 P16117
- Elsewhere: RCSB PDB 1PER · PDBe 1PER · UniProt P16117
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