MolNFT v1 · #172051 · RNA
Racemic compound of RNA duplexes.
6ZPF · RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3'): “Racemic compound of RNA duplexes.”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.31). MolNFT v1 #172051 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZPF
- Type
- RNA
- Length
- 32 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3'); RNA (5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3'); RNA…
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.31
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3') | rna | 8 | — | — |
| L | RNA (5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3') | rna | 8 | — | — |
| M, N | RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))- 3') | rna | 8 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains K, M, L, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.31 | 0.73 | 12 | ZN |
| 2 | 71 | 0.27 | 0.73 | 10 | ZN |
Interfaces
6 interfaces between chains.
- K–L · 421 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- M–N · 420 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- L–N · 121 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- K–M · 116 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- K–N · 44 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 16 modified (nucleotide modification).
Compared structures
- 6ZPF · Racemic compound of RNA duplexes. · the same entry in another collection · chain K against K, 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 6ZPF · PDBe 6ZPF
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