Research workbench
Structure of proteinaceous RNase P 1 (PRORP1) from a. thaliana complexed with mn after 3-hour soak with juglone
Analyse Structure of proteinaceous RNase P 1 (PRORP1) from a. thaliana complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BV8
- Type
- protein
- Length
- 472 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteinaceous RNase P 1, CHLOROPLASTIC/MITOCHONDRIAL
- EC
- 3.1.26.5
- UniProt
- Q66GI4
- Ligands
- JUG, MN, ZN, CL
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proteinaceous RNase P 1, CHLOROPLASTIC/MITOCHONDRIAL (EC 3.1.26.5) | protein | 472 | 53% helix, 11% strand | Q66GI4 |
Ligands and binding sites
- JUG · 5-hydroxynaphthalene-1,4-dione · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.71 | 0.80 | 52 | empty |
| 2 | 93 | 0.49 | 0.82 | 21 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6BV8 · Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana complexed with Mn after… · the same entry in another collection · chain A against A, TM-score 1.00
- Q66GI4 · AlphaFold monomer V2.0 prediction for proteinaceous RNase P 1… · a predicted model of the same protein · chain A against A, TM-score 0.93
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 6BV8 · PDBe 6BV8 · UniProt Q66GI4
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