Research workbench
Crystal structure of RNA-10MER: CCGG(N4-methyl-C)GCCGG
Analyse Crystal structure of RNA-10MER: CCGG(N4-methyl-C)GCCGG in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WY2
- Type
- RNA
- Length
- 50 nucleotides
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-10MER: CCGG(4-methyl-C)GCCGG
- Ligands
- MG, K
- Pockets
- 2 · best druggability 0.29
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | RNA-10MER: CCGG(4-methyl-C)GCCGG | rna | 10 | — | — |
Ligands and binding sites
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 | 91 | 0.29 | 0.72 | 10 | MG |
| 2 | 72 | 0.27 | 0.73 | 10 | MG |
Interfaces
8 interfaces between chains.
- D–E · 537 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- B–C · 528 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- C–D · 112 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- A–C · 111 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- B–E · 110 Ų buried · 5 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 5 modified (nucleotide modification).
Compared structures
- 6WY2 · Crystal structure of RNA-10mer: CCGG(N4-methyl-C)GCCGG · 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 6WY2 · PDBe 6WY2
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