MolNFT v1 · #108863 · DNA + RNA
Crystallographic structure of a dodecameric RNA-DNA hybrid
4WKJ · RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3'): “Crystallographic structure of a dodecameric RNA-DNA hybrid”. X-ray diffraction, 1 ligand (MG), 5 pockets (best druggability 0.40). MolNFT v1 #108863 on GenesisL1: 3D structure…
- PDB
- 4WKJ
- Type
- DNA + RNA
- Length
- 96 nucleotides
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3'); DNA…
- Ligands
- MG
- Pockets
- 5 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, C, G | RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3') | rna | 12 | — | — |
| E, B, F, H | DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.40 | 0.78 | 14 | empty |
| 2 | 160 | 0.36 | 0.72 | 13 | empty |
| 3 | 121 | 0.32 | 0.71 | 14 | MG |
| 4 | 105 | 0.31 | 0.72 | 12 | empty |
| 5 | 91 | 0.29 | 0.72 | 10 | empty |
Interfaces
12 interfaces between chains.
- C–F · 554 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- A–B · 550 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- D–E · 550 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- G–H · 549 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- E–A · 125 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Compared structures
- 4WKJ · Crystallographic Structure of a Dodecameric RNA-DNA Hybrid · the same entry in another collection · chain D against D, 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
- Elsewhere: RCSB PDB 4WKJ · PDBe 4WKJ
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