MolNFT v1 · #172235 · RNA
Racemic compound of RNA duplexes.
6ZW3 · RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))…: “Racemic compound of RNA duplexes.”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.30). MolNFT v1 #172235 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6ZW3
- Type
- RNA
- Length
- 32 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))- 3'); RNA…
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.30
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K, L | RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))- 3') | rna | 8 | — | — |
| M | RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3') | rna | 8 | — | — |
| N | RNA (5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3') | rna | 8 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains K, L, M, 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 | 84 | 0.30 | 0.73 | 10 | ZN |
| 2 | 77 | 0.29 | 0.73 | 11 | ZN |
Interfaces
6 interfaces between chains.
- M–N · 427 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- K–L · 422 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- L–N · 118 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- K–M · 115 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
- 6ZW3 · 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 6ZW3 · PDBe 6ZW3
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