Research workbench
Crystal structure of the ppr domain of arabidopsis thaliana protein- only RNase P 1 (PRORP1) in complex with tRNA
Analyse Crystal structure of the ppr domain of arabidopsis thaliana protein- only RNase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LVR
- Type
- protein + RNA
- Length
- 531 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteinaceous RNase P 1, CHLOROPLASTIC/MITOCHONDRIAL; Yeast phenylalanine tRNA
- EC
- 3.1.26.5
- UniProt
- Q66GI4
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Proteinaceous RNase P 1, CHLOROPLASTIC/MITOCHONDRIAL (EC 3.1.26.5) | protein | 194 | 75% helix, 0% strand | Q66GI4 |
| A | Proteinaceous RNase P 1, CHLOROPLASTIC/MITOCHONDRIAL (EC 3.1.26.5) | protein | 193 | 74% helix, 0% strand | Q66GI4 |
| D, B | Yeast phenylalanine tRNA | rna | 72 | — | — |
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.82 | 0.84 | 106 | empty |
| 2 | 714 | 0.64 | 0.75 | 32 | empty |
| 3 | 666 | 0.64 | 0.75 | 39 | empty |
| 4 | 328 | 0.55 | 0.76 | 20 | empty |
| 5 | 335 | 0.55 | 0.76 | 20 | empty |
Interfaces
4 interfaces between chains.
- C–A · 935 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 646 Ų buried · 17 hydrogen bonds · protein-nucleic
- C–D · 542 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–B · 245 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 28 modified (nucleotide modification).
Compared structures
- 6LVR · Crystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1… · the same entry in another collection · chain C against C, TM-score 1.00
- Q66GI4 · AlphaFold monomer V2.0 prediction for proteinaceous RNase P 1… · a predicted model of the same protein · chain C against A, TM-score 0.96
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 Q66GI4
- Elsewhere: RCSB PDB 6LVR · PDBe 6LVR · UniProt Q66GI4
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