Research workbench
Structure of the mRNA-binding domain of elongation factor selb from E.COLI in complex with secis RNA
Analyse Structure of the mRNA-binding domain of elongation factor selb from E.COLI in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PJP
- Type
- protein + RNA
- Length
- 144 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Selenocysteine-specific elongation factor; Secis RNA
- UniProt
- P14081
- Ligands
- MG, CA, NA, CL
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Selenocysteine-specific elongation factor | protein | 121 | 60% helix, 17% strand | P14081 |
| B | Secis RNA | rna | 23 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 17 copies · chains B, A
- CA · Calcium ion · metal · 4 copies · chains A
- NA · Sodium ion · metal
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.50 | 0.75 | 23 | MG |
Interfaces
1 interface between chains.
- A–B · 654 Ų buried · 24 hydrogen bonds · protein-nucleic
Compared structures
- 2PJP · Structure of the mRNA-binding domain of elongation factor SelB from E.coli in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P14081 · AlphaFold monomer V2.0 prediction for selenocysteine-specific elongation factor (P14081) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P14081
- Elsewhere: RCSB PDB 2PJP · PDBe 2PJP · UniProt P14081
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