Research workbench
Crystal structure of the homo sapiens mitochondrial ribosomal decoding site in the presence of nonspecifically bound paromomycin (A1555G mutant, br-derivative)
Analyse Crystal structure of the homo sapiens mitochondrial ribosomal decoding site in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BNR
- Type
- RNA
- Length
- 89 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A site of human mitochondrial ribosome, chain one; A site of human mitochondrial…
- Ligands
- PAR, K
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | A site of human mitochondrial ribosome, chain one | rna | 23 | — | — |
| B | A site of human mitochondrial ribosome, chain two | rna | 22 | — | — |
| D | A site of human mitochondrial ribosome, chain three | rna | 21 | — | — |
Ligands and binding sites
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 | 614 | 0.60 | 0.74 | 38 | empty |
| 2 | 337 | 0.50 | 0.73 | 26 | empty |
| 3 | 269 | 0.47 | 0.73 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 948 Ų buried · 88 hydrogen bonds · nucleic-nucleic
- C–D · 947 Ų buried · 97 hydrogen bonds · nucleic-nucleic
- B–D · 220 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- A–C · 181 Ų buried · 8 hydrogen bonds · nucleic-nucleic
- A–D · 172 Ų buried · 3 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 3BNR · Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the… · 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 3BNR · PDBe 3BNR
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