MolNFT v1 · #5392 · DNA + RNA
Crystal structure of a nucleic acid four-way junction
1EGK · RNA (5'- R(*AP*GP*GP*AP*GP*AP*GP*AP*GP*AP*UP*GP*GP*GP*UP*GP*…: “Crystal structure of a nucleic acid four-way junction”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.69). MolNFT v1 #5392 on GenesisL1: 3D…
- PDB
- 1EGK
- Type
- DNA + RNA
- Length
- 108 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'- R(*AP*GP*GP*AP*GP*AP*GP*AP*GP*AP*UP*GP*GP*GP*UP*GP*CP*GP*AP*G)-3'); 10-23 DNA…
- Ligands
- MG
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RNA (5'- R(*AP*GP*GP*AP*GP*AP*GP*AP*GP*AP*UP*GP*GP*GP*UP*GP*CP*GP*AP*G)-3') | rna | 20 | — | — |
| B, D | 10-23 DNA enzyme | dna | 34 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 14 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.69 | 0.75 | 43 | MG |
| 2 | 986 | 0.66 | 0.73 | 37 | MG |
| 3 | 110 | 0.44 | 0.79 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–D · 728 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- B–C · 695 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- B–D · 572 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- C–D · 533 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- A–B · 523 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Compared structures
- 1EGK · Crystal structure of a nucleic acid four-way junction · 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
- Elsewhere: RCSB PDB 1EGK · PDBe 1EGK
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