MolNFT v1 · #11881 · RNA
Crystal structure of a bulged RNA from the SL2 stem-loop of the HIV-1 psi-RNA
1JZV · 5'-R(*GP*GP*CP*GP*AP*CP*(5BU)P*G)-3': “Crystal structure of a bulged RNA from the SL2 stem-loop of the HIV-1 psi-RNA”. X-ray diffraction, 1 ligand (MG). MolNFT v1 #11881 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1JZV
- Type
- RNA
- Length
- 34 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*GP*GP*CP*GP*AP*CP*(5BU)P*G)-3'; 5'-R(*CP*AP*GP*UP*AP*CP*GP*(5IC)P*C)-3'
- Ligands
- MG
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 5'-R(*GP*GP*CP*GP*AP*CP*(5BU)P*G)-3' | rna | 8 | — | — |
| B, D | 5'-R(*CP*AP*GP*UP*AP*CP*GP*(5IC)P*C)-3' | rna | 9 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
5 interfaces between chains.
- C–D · 412 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- A–B · 411 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- B–D · 279 Ų buried · 7 hydrogen bonds · nucleic-nucleic
- B–C · 166 Ų buried · 5 hydrogen bonds · nucleic-nucleic
- A–D · 162 Ų buried · 5 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 1JZV · Crystal structure of a bulged RNA from the SL2 stem-loop of the HIV-1 psi-RNA · 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 1JZV · PDBe 1JZV
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