Research workbench
DNA-binding domain of deor in complex with the DNA operator
Analyse DNA-binding domain of deor in complex with the DNA operator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BHY
- Type
- protein + DNA
- Length
- 195 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA operator - strand 1; DNA operator - strand 2; Deoxyribonucleoside regulator
- UniProt
- P39140
- Ligands
- PO4
- Pockets
- 1 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 67% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | DNA operator - strand 1 | dna | 15 | — | — |
| G | DNA operator - strand 2 | dna | 15 | — | — |
| A | Deoxyribonucleoside regulator | protein | 57 | 68% helix, 9% strand | P39140 |
| B | Deoxyribonucleoside regulator | protein | 53 | 64% helix, 9% strand | P39140 |
| C | Deoxyribonucleoside regulator | protein | 55 | 67% helix, 0% strand | P39140 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.79 | 0.81 | 70 | empty |
Interfaces
9 interfaces between chains.
- E–G · 669 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- A–B · 668 Ų buried · 9 hydrogen bonds · protein-protein
- G–B · 314 Ų buried · 7 hydrogen bonds · protein-nucleic
- E–A · 300 Ų buried · 7 hydrogen bonds · protein-nucleic
- G–A · 227 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 7BHY · DNA-binding domain of DeoR in complex with the DNA operator · the same entry in another collection · chain C against C, TM-score 1.00
- P39140 · AlphaFold monomer V2.0 prediction for deoxyribonucleoside regulator (P39140) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 P39140
- Elsewhere: RCSB PDB 7BHY · PDBe 7BHY · UniProt P39140
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