Research workbench
Variant 1 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle
Analyse Variant 1 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PXD
- Type
- protein + RNA
- Length
- 118 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Escherichia coli; SYNTHETIC CONSTRUCT
- Molecule
- 4.5 S RNA; Signal recognition particle protein
- UniProt
- P0AGD7
- Ligands
- NCO
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · resolution 2 · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 4.5 S RNA | rna | 49 | — | — |
| A | Signal recognition particle protein | protein | 69 | 71% helix, 0% strand | P0AGD7 |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 7 copies · chains B
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 | 345 | 0.56 | 0.76 | 22 | NCO |
| 2 | 238 | 0.46 | 0.74 | 19 | NCO |
Interfaces
1 interface between chains.
- B–A · 638 Ų buried · 25 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2PXD · Variant 1 of ribonucleoprotein core of the E. COLI signal recognition particle · the same entry in another collection · chain A against A, TM-score 1.00
- P0AGD7 · AlphaFold monomer V2.0 prediction for signal recognition particle protein (P0AGD7) · a predicted model of the same protein · chain A 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 P0AGD7
- Elsewhere: RCSB PDB 2PXD · PDBe 2PXD · UniProt P0AGD7
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