Research workbench
Crystal structure of bioq with its naturel double-stranded DNA operator
Analyse Crystal structure of bioq with its naturel double-stranded DNA operator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YEJ
- Type
- protein + DNA
- Length
- 560 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetr family transcriptional regulator; DNA (5'…
- UniProt
- I7FDJ0
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tetr family transcriptional regulator | protein | 169 | 75% helix, 0% strand | I7FDJ0 |
| B | Tetr family transcriptional regulator | protein | 165 | 76% helix, 0% strand | I7FDJ0 |
| D, G | DNA (5'- D(*AP*CP*CP*TP*GP*AP*AP*CP*AP*CP*CP*GP*TP*TP*CP*AP*AP*GP*T)-3') | dna | 19 | — | — |
| F | DNA (5'- D(*AP*CP*TP*TP*GP*AP*AP*CP*GP*GP*TP*GP*TP*TP*CP*AP*GP*GP*T)-3') | dna | 19 | — | — |
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 | 618 | 0.70 | 0.78 | 47 | empty |
| 2 | 85 | 0.40 | 0.78 | 13 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1059 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 846 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- D–C · 422 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–D · 383 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–G · 377 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 5YEJ · Crystal structure of BioQ with its naturel double-stranded DNA operator · 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 I7FDJ0
- Elsewhere: RCSB PDB 5YEJ · PDBe 5YEJ · UniProt I7FDJ0
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