Research workbench
3.0 a structure of fragment I from E. COLI 5S rRNA
Analyse 3.0 a structure of fragment I from E. COLI 5S rRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 364D
- Type
- RNA
- Length
- 60 nucleotides
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*UP*GP*)-D(*(1SC)P*)- R(*CP*UP*GP*GP*CP*GP*GP*C)-3'); RNA (5'…
- Ligands
- MG
- Pockets
- 2 · best druggability 0.31
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (5'-R(*UP*GP*)-D(*(1SC)P*)- R(*CP*UP*GP*GP*CP*GP*GP*C)-3') | rna | 11 | — | — |
| B | RNA (5'- R(*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*GP*UP*GP*GP*GP*G *UP*C)-3') | rna | 19 | — | — |
| C | RNA (5'- R(*CP*CP*CP*CP*AP*UP*GP*CP*GP*AP*GP*AP*GP*UP*AP*GP*G P*GP*AP*AP*CP*UP*GP*CP*CP*AP*GP*GP*CP*AP*U)-3') | rna | 30 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 12 copies · chains A, B, C
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 | 113 | 0.31 | 0.71 | 12 | MG |
| 2 | 50 | 0.23 | 0.73 | 9 | MG |
Interfaces
2 interfaces between chains.
- B–C · 1093 Ų buried · 105 hydrogen bonds · nucleic-nucleic
- A–C · 571 Ų buried · 70 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 364D · 3.0 a structure of fragment I from E. COLI 5S rRNA · 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 364D · PDBe 364D
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