Research workbench
Variant 13 of ribonucleoprotein core of the E. COLI signal recognition particle
Analyse Variant 13 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
- 2PXP
- Type
- protein + RNA
- Length
- 118 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4.5 S RNA; Signal recognition particle protein
- UniProt
- P0AGD7
- Ligands
- NCO
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 70% 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 | 70% 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 | 332 | 0.55 | 0.76 | 24 | NCO |
| 2 | 269 | 0.48 | 0.74 | 20 | NCO |
Interfaces
1 interface between chains.
- B–A · 643 Ų buried · 24 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2PXP · Variant 13 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle · the same entry in another collection · chain B against B, 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 0.97
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 2PXP · PDBe 2PXP · UniProt P0AGD7
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