Research workbench
Safadr in complex with dsdna
Analyse Safadr in complex with dsdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EN8
- Type
- protein + DNA
- Length
- 1,205 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator tetr family; DNA (5'…
- UniProt
- Q4J9S1
- Ligands
- UNL
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 7 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Transcriptional regulator tetr family | protein | 191 | 78% helix, 0% strand | Q4J9S1 |
| B | Transcriptional regulator tetr family | protein | 184 | 79% helix, 0% strand | Q4J9S1 |
| D | Transcriptional regulator tetr family | protein | 175 | 80% helix, 0% strand | Q4J9S1 |
| E | Transcriptional regulator tetr family | protein | 191 | 76% helix, 0% strand | Q4J9S1 |
| F | Transcriptional regulator tetr family | protein | 189 | 74% helix, 0% strand | Q4J9S1 |
| Q, Y | DNA (5'- D(*GP*TP*CP*GP*AP*CP*TP*CP*AP*AP*AP*AP*AP*TP*CP*AP*AP*GP*TP*AP*G)- 3') | dna | 21 | — | — |
| X, Z | DNA (5'- D(*CP*TP*AP*CP*TP*TP*GP*AP*TP*TP*TP*TP*TP*GP*AP*GP*TP*CP*GP*AP*C)- 3') | dna | 21 | — | — |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.75 | 0.86 | 44 | empty |
| 2 | 172 | 0.71 | 0.89 | 25 | empty |
| 3 | 285 | 0.70 | 0.84 | 32 | empty |
| 4 | 256 | 0.69 | 0.85 | 34 | empty |
| 5 | 759 | 0.69 | 0.76 | 57 | empty |
Interfaces
22 interfaces between chains.
- A–B · 1974 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1859 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1847 Ų buried · 16 hydrogen bonds · protein-protein
- X–Y · 935 Ų buried · 86 hydrogen bonds · nucleic-nucleic
- Q–Z · 924 Ų buried · 85 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 42 modified (engineered).
Compared structures
- 6EN8 · SaFadR in complex with dsDNA · 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 Q4J9S1
- Elsewhere: RCSB PDB 6EN8 · PDBe 6EN8 · UniProt Q4J9S1
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