MolNFT v1 · #48201 · protein + RNA
Structure of the mRNA binding fragment of elongation factor selb in complex with secis RNA.
2PLY · RNA (5'- R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP*GP*UP*CP*UP*GP*GP*…: “Structure of the mRNA binding fragment of elongation factor selb in complex with secis RNA.”. X-ray diffraction, 4 ligands (MG, CA, NA), 6 pockets (best druggability…
- 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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