MolNFT v1 · #75821 · protein + RNA
Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA
3Q1Q · RNase P RNA: “Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA”. X-ray diffraction, 2 ligands (MG, PO4), 20 pockets (best druggability 0.78). MolNFT v1 #75821 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3Q1Q
- Type
- protein + RNA
- Length
- 545 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNase P RNA; Ribonuclease P protein component; TRNA (phe)
- EC
- 3.1.26.5
- UniProt
- Q9X1H4
- Ligands
- MG, PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RNase P RNA | rna | 347 | — | — |
| A | Ribonuclease P protein component (EC 3.1.26.5) | protein | 112 | 46% helix, 21% strand | Q9X1H4 |
| C | TRNA (phe) | rna | 86 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains C, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.78 | 0.85 | 33 | empty |
| 2 | 113 | 0.75 | 0.96 | 21 | empty |
| 3 | 332 | 0.70 | 0.84 | 35 | PO4 |
| 4 | 348 | 0.69 | 0.83 | 26 | empty |
| 5 | 406 | 0.66 | 0.80 | 34 | MG |
Interfaces
2 interfaces between chains.
- B–C · 1443 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- B–A · 1318 Ų buried · 35 hydrogen bonds · protein-nucleic
Compared structures
- 3Q1Q · Structure of a Bacterial Ribonuclease P Holoenzyme in Complex with tRNA · the same entry in another collection · chain B against B, TM-score 1.00
- Q9X1H4 · AlphaFold monomer V2.0 prediction for ribonuclease P protein component (Q9X1H4) · 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 Q9X1H4
- Elsewhere: RCSB PDB 3Q1Q · PDBe 3Q1Q · UniProt Q9X1H4
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