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Structure of the mRNA binding fragment of elongation factor selb in complex with secis RNA.
Analyse Structure of the mRNA binding fragment of elongation factor selb in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PLY
- Type
- protein + RNA
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'- R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP*GP*UP*CP*UP*GP*GP*CP*AP*AP*CP*GP*CP* C)-3')…
- UniProt
- Q46455
- Ligands
- MG, CA, NA, CL
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | RNA (5'- R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP*GP*UP*CP*UP*GP*GP*CP*AP*AP*CP*GP*CP* C)-3') | rna | 23 | — | — |
| A | Selenocysteine-specific elongation factor | protein | 212 | 55% helix, 15% strand | Q46455 |
| B | Selenocysteine-specific elongation factor | protein | 198 | 58% helix, 12% strand | Q46455 |
Ligands and binding sites
- MG · Magnesium ion · metal · 17 copies · chains C, A, B, E
- CA · Calcium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains C, A
- CL · Chloride ion · ion · 4 copies · chains A, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.74 | 0.78 | 57 | MG, CL |
| 2 | 691 | 0.68 | 0.77 | 48 | MG |
| 3 | 105 | 0.39 | 0.75 | 18 | empty |
| 4 | 107 | 0.39 | 0.75 | 19 | CA |
| 5 | 56 | 0.37 | 0.80 | 12 | MG |
Interfaces
5 interfaces between chains.
- C–A · 612 Ų buried · 14 hydrogen bonds · protein-nucleic
- E–B · 485 Ų buried · 8 hydrogen bonds · protein-nucleic
- E–A · 484 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–B · 445 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–B · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2PLY · Structure of the mRNA binding fragment of elongation factor SelB in complex with SECIS… · the same entry in another collection · chain C against C, TM-score 1.00
- Q46455 · AlphaFold monomer V2.0 prediction for selenocysteine-specific elongation factor (Q46455) · a predicted model of the same protein · chain B against A, TM-score 0.64
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 Q46455
- Elsewhere: RCSB PDB 2PLY · PDBe 2PLY · UniProt Q46455
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