MolNFT v1 · #134417 · RNA
Fluorescence detection of RNA-ligand binding and crystal structure determination of ribosomal decoding site RNA using a heavy atom containing fluorescent ribonucleoside
5T3K · RNA (5'- R(*GP*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*UP*GP*…: “Fluorescence detection of RNA-ligand binding and crystal structure determination of ribosomal decoding site…”. X-ray diffraction, 1 ligand (MG), 3 pockets (best…
- PDB
- 5T3K
- Type
- RNA
- Length
- 66 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'- R(*GP*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*UP*GP*G)-3'); RNA…
- Ligands
- MG
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RNA (5'- R(*GP*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*UP*GP*G)-3') | rna | 17 | — | — |
| B, D | RNA (5'-R(*CP*AP*GP*CP*GP*(75B) P*CP*AP*CP*AP*CP*CP*AP*CP*CP*C)-3') | rna | 16 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.57 | 0.74 | 30 | MG |
| 2 | 443 | 0.55 | 0.74 | 27 | MG |
| 3 | 50 | 0.24 | 0.74 | 10 | empty |
Interfaces
5 interfaces between chains.
- A–B · 800 Ų buried · 80 hydrogen bonds · nucleic-nucleic
- C–D · 787 Ų buried · 80 hydrogen bonds · nucleic-nucleic
- B–C · 135 Ų buried · 1 hydrogen bond · nucleic-nucleic
- A–D · 94 Ų buried · 1 hydrogen bond · nucleic-nucleic
- A–C · 80 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5T3K · Fluorescence detection of RNA-ligand binding and crystal structure determination of… · 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 5T3K · PDBe 5T3K
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