Research workbench
Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the BPUJ1 endonuclease binding domain
Analyse Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HNF
- Type
- protein + DNA
- Length
- 300 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Restriction endonuclease R.BPUJI; DNA (5'-D(*GP*(YPE)P*AP*CP*CP*CP*GP*TP*GP*GP*A)-3')…
- UniProt
- A3FMN7
- Ligands
- YPE, YPF
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Restriction endonuclease R.BPUJI | protein | 280 | 59% helix, 9% strand | A3FMN7 |
| L | DNA (5'-D(*GP*(YPE)P*AP*CP*CP*CP*GP*TP*GP*GP*A)-3') | dna | 10 | — | — |
| M | DNA (5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*TP*(YPF)P*C)-3') | dna | 10 | — | — |
Ligands and binding sites
- YPE · 4-[8-(4-hydroxybut-1-yn-1-yl)pyren-1-yl]but-3-yn-1-yl dihydrogen phosphate · ligand · chains L, M
- YPF · 4-[6-(4-oxidanylbut-1-ynyl)phenanthren-3-yl]but-3-ynyl dihydrogen phosphate · ligand · chains A, L, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.71 | 0.85 | 28 | empty |
| 2 | 152 | 0.52 | 0.79 | 21 | empty |
| 3 | 117 | 0.37 | 0.74 | 22 | empty |
| 4 | 56 | 0.25 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–M · 798 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–L · 689 Ų buried · 12 hydrogen bonds · protein-nucleic
- L–M · 460 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5HNF · Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the BpuJ1… · 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 A3FMN7
- Elsewhere: RCSB PDB 5HNF · PDBe 5HNF · UniProt A3FMN7
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