Research workbench
Crystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 1)
Analyse Crystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P3U
- Type
- RNA
- Length
- 86 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU) P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU) P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3' | rna | 21 | — | — |
| B, C | 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU) P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3' | rna | 22 | — | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.53 | 0.73 | 27 | empty |
| 2 | 261 | 0.44 | 0.72 | 22 | empty |
| 3 | 195 | 0.41 | 0.72 | 19 | empty |
| 4 | 80 | 0.27 | 0.72 | 11 | empty |
Interfaces
2 interfaces between chains.
- C–D · 974 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- A–B · 964 Ų buried · 70 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 4P3U · Crystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 1) · 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 4P3U · PDBe 4P3U
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