MolNFT v1 · #176310 · protein + RNA
Mycoplasma genitalium RNase R in complex with ribose methylated single-stranded RNA
7DID · Ribonuclease R: “Mycoplasma genitalium RNase R in complex with ribose methylated single-stranded RNA”. X-ray diffraction, 1 ligand (MG), 8 pockets (best druggability 0.81). MolNFT v1 #176310 on GenesisL1: 3D structure, binding sites…
- PDB
- 7DID
- Type
- protein + RNA
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease R; RNA (5'-R(*AP*AP*AP*A)-3')
- EC
- 3.1.13.1
- UniProt
- P47350
- Ligands
- MG
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease R (EC 3.1.13.1) | protein | 644 | 32% helix, 31% strand | P47350 |
| C | RNA (5'-R(*AP*AP*AP*A)-3') | rna | 4 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.81 | 0.82 | 113 | empty |
| 2 | 163 | 0.66 | 0.87 | 25 | empty |
| 3 | 105 | 0.45 | 0.79 | 16 | empty |
| 4 | 67 | 0.43 | 0.81 | 17 | empty |
| 5 | 99 | 0.43 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–C · 752 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7DID · Mycoplasma genitalium RNase R in complex with ribose methylated single-stranded RNA · the same entry in another collection · chain A against A, TM-score 1.00
- P47350 · AlphaFold monomer V2.0 prediction for ribonuclease R (P47350) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P47350
- Elsewhere: RCSB PDB 7DID · PDBe 7DID · UniProt P47350
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