Research workbench
Recognition of at-rich DNA binding sites by the mogr repressor
Analyse Recognition of at-rich DNA binding sites by the mogr repressor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FDQ
- Type
- protein + DNA
- Length
- 310 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Motility gene repressor mogr; 5'- D(*AP*TP*TP*TP*TP*TP*TP*AP*AP*AP*AP*AP*AP*AP*T)-3'; 5'…
- UniProt
- Q8Y960
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 61% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Motility gene repressor mogr | protein | 140 | 61% helix, 4% strand | Q8Y960 |
| C | 5'- D(*AP*TP*TP*TP*TP*TP*TP*AP*AP*AP*AP*AP*AP*AP*T)-3' | dna | 15 | — | — |
| D | 5'- D(*TP*AP*TP*TP*TP*TP*TP*TP*TP*AP*AP*AP*AP*AP*A)-3' | dna | 15 | — | — |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.74 | 0.79 | 41 | empty |
| 2 | 143 | 0.57 | 0.82 | 22 | empty |
| 3 | 166 | 0.55 | 0.81 | 20 | empty |
| 4 | 121 | 0.46 | 0.78 | 19 | empty |
| 5 | 77 | 0.35 | 0.76 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–D · 680 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 621 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- B–C · 612 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 528 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–D · 524 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 3FDQ · Recognition of AT-rich DNA binding sites by the MogR Repressor · 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 Q8Y960
- Elsewhere: RCSB PDB 3FDQ · PDBe 3FDQ · UniProt Q8Y960
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