MolNFT v1 · #127051 · RNA
Crystal structure of L1-stalk fragment of 23S rRNA from haloarcula marismortui
5ML7 · 23S ribosomal RNA: “Crystal structure of L1-stalk fragment of 23S rRNA from haloarcula marismortui”. X-ray diffraction, 2 ligands (MG, CA), 7 pockets (best druggability 0.73). MolNFT v1 #127051 on GenesisL1: 3D structure, binding…
- PDB
- 5ML7
- Type
- RNA
- Length
- 190 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA
- Ligands
- MG, CA
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 23S ribosomal RNA | rna | 95 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.73 | 0.77 | 61 | CA, MG |
| 2 | 822 | 0.71 | 0.78 | 42 | MG |
| 3 | 339 | 0.56 | 0.76 | 20 | empty |
| 4 | 134 | 0.45 | 0.78 | 15 | empty |
| 5 | 107 | 0.36 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 305 Ų buried · 5 hydrogen bonds · nucleic-nucleic
Compared structures
- 5ML7 · CRYSTAL STRUCTURE OF L1-STALK FRAGMENT OF 23S rRNA FROM HALOARCULA MARISMORTUI · the same entry in another collection · chain B against B, 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 5ML7 · PDBe 5ML7
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