Research workbench
Structure of the cytosolic protein pym bound to the mago-Y14 core of the exon junction complex
Analyse Structure of the cytosolic protein pym bound to the mago-Y14 core of the exon… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RK8
- Type
- protein
- Length
- 247 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CG8781-pa protein; Mago nashi protein; Within the bgcn gene intron protein
- UniProt
- Q9V535, P49028, P82804
- Ligands
- CA
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CG8781-pa protein | protein | 87 | 25% helix, 38% strand | Q9V535 |
| B | Mago nashi protein | protein | 127 | 36% helix, 31% strand | P49028 |
| C | Within the bgcn gene intron protein | protein | 33 | 0% helix, 39% strand | P82804 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.54 | 0.83 | 18 | empty |
| 2 | 115 | 0.40 | 0.76 | 22 | empty |
| 3 | 56 | 0.31 | 0.76 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1189 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 420 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 372 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1RK8 · Structure of the cytosolic protein PYM bound to the Mago-Y14 core of the exon junction… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9V535 · AlphaFold monomer V2.0 prediction for RNA-binding protein 8A (Q9V535) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P49028 · AlphaFold monomer V2.0 prediction for protein mago nashi (P49028) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P82804 · AlphaFold monomer V2.0 prediction for partner of Y14 and mago (P82804) · a predicted model of the same protein · chain C against A, TM-score 0.90
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 Q9V535
- Every structure of UniProt P49028
- Every structure of UniProt P82804
- Elsewhere: RCSB PDB 1RK8 · PDBe 1RK8 · UniProt Q9V535 · UniProt P49028 · UniProt P82804
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