MolNFT v1 · #107310 · DNA + RNA
Crystal structure of DNA/RNA duplex containing 2'-4'-bna-nc
4U6K · RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3'): “Crystal structure of DNA/RNA duplex containing 2'-4'-bna-nc”. X-ray diffraction, 1 ligand (NCO), 1 pocket (best druggability 0.29). MolNFT v1 #107310 on GenesisL1: 3D structure, binding…
- PDB
- 4U6K
- Type
- DNA + RNA
- Length
- 36 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3'); DNA…
- Ligands
- NCO
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3') | rna | 9 | — | — |
| B, D | DNA (5'-D(*(NCU)P*(NTT)P*CP*TP*TP*CP*TP*(NTT)P*(NCU))-3') | dna | 9 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.29 | 0.72 | 9 | NCO |
Interfaces
6 interfaces between chains.
- C–D · 437 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- A–B · 432 Ų buried · 38 hydrogen bonds · nucleic-nucleic
- B–D · 84 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- B–C · 80 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- A–D · 74 Ų buried · 1 hydrogen bond · nucleic-nucleic
Modifications
Observed in the structure: 8 modified (nucleotide modification).
Compared structures
- 4U6K · Crystal structure of DNA/RNA duplex containing 2'-4'-BNA-NC · 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 4U6K · PDBe 4U6K
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