MolNFT v1 · #121175 · protein + DNA
Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the BPUJ1 endonuclease binding domain
5HNH · Restriction endonuclease R.BPUJI: “Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the BPUJ1 endonuclease binding…”. X-ray diffraction, 1 ligand (YPE), 4 pockets (best druggability 0.56). MolNFT v1 #121175…
- PDB
- 5HNH
- Type
- protein + DNA
- Length
- 299 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Restriction endonuclease R.BPUJI; DNA (5'-D(*GP*(YPY)P*AP*CP*CP*CP*GP*TP*GP*GP*A)-3')…
- UniProt
- A3FMN7
- Ligands
- YPE
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Restriction endonuclease R.BPUJI | protein | 279 | 58% helix, 9% strand | A3FMN7 |
| L | DNA (5'-D(*GP*(YPY)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*T*(YPY)*(YPY)*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 · 3 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.56 | 0.77 | 27 | empty |
| 2 | 113 | 0.48 | 0.80 | 18 | empty |
| 3 | 124 | 0.37 | 0.74 | 19 | empty |
| 4 | 51 | 0.25 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–L · 762 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–M · 661 Ų buried · 21 hydrogen bonds · protein-nucleic
- L–M · 506 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5HNH · 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 5HNH · PDBe 5HNH · UniProt A3FMN7
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