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Crystal structure of an RNA domain from hepatitis C virus.
Analyse Crystal structure of an RNA domain from hepatitis C virus. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NOK
- Type
- RNA
- Length
- 88 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP *CP*AP*CP*GP*CP*C)-3'…
- Ligands
- MG, MN
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP *CP*AP*CP*GP*CP*C)-3' | rna | 24 | — | — |
| B, D | 5'-R(*GP*CP*GP*UP*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*UP*CP*CP *GP*G)-3' | rna | 20 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains B, A, C, D
- MN · Manganese (II) ion · metal · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.69 | 0.87 | 17 | MG |
| 2 | 643 | 0.64 | 0.75 | 29 | MN, MG |
| 3 | 547 | 0.61 | 0.75 | 31 | MN, MG |
| 4 | 78 | 0.27 | 0.72 | 15 | MG |
| 5 | 51 | 0.22 | 0.72 | 12 | MG |
Interfaces
6 interfaces between chains.
- C–D · 1056 Ų buried · 114 hydrogen bonds · nucleic-nucleic
- A–B · 1040 Ų buried · 106 hydrogen bonds · nucleic-nucleic
- A–C · 311 Ų buried · 10 hydrogen bonds · nucleic-nucleic
- B–C · 84 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- A–D · 71 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Compared structures
- 2NOK · Crystal Structure of an RNA domain from Hepatitis C virus. · 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 2NOK · PDBe 2NOK
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