Research workbench
Crystal Structure of nuclear proteinaceous RNase P 2 (PRORP2) from A. thaliana
Analyse Crystal Structure of nuclear proteinaceous RNase P 2 (PRORP2) from A. thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DIZ
- Type
- protein
- Length
- 946 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Arabidopsis thaliana
- Molecule
- Proteinaceous RNase P 2
- EC
- 3.1.26.5
- UniProt
- Q680B9
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · resolution 3.2 · 2 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proteinaceous RNase P 2 (EC 3.1.26.5) | protein | 474 | 50% helix, 11% strand | Q680B9 |
| B | Proteinaceous RNase P 2 (EC 3.1.26.5) | protein | 472 | 51% helix, 10% strand | Q680B9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.65 | 0.77 | 46 | empty |
| 2 | 412 | 0.64 | 0.78 | 48 | empty |
| 3 | 353 | 0.60 | 0.77 | 30 | empty |
| 4 | 53 | 0.55 | 0.89 | 15 | empty |
| 5 | 108 | 0.43 | 0.78 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 932 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5DIZ · Crystal structure of nuclear proteinaceous RNase P 2 (PRORP2) from a. thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- Q680B9 · AlphaFold monomer V2.0 prediction for proteinaceous RNase P 2 (Q680B9) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q680B9
- Elsewhere: RCSB PDB 5DIZ · PDBe 5DIZ · UniProt Q680B9
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