Research workbench
Structure of the human exon junction complex with a trapped dead-box helicase bound to RNA
Analyse Structure of the human exon junction complex with a trapped dead-box helicase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HYI
- Type
- protein + RNA
- Length
- 1,373 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*UP*UP*UP*UP*UP*U)-3'; Protein mago nashi homolog; RNA-binding protein 8A; Probable…
- EC
- 3.6.1.-
- UniProt
- P61326, Q9Y5S9, P38919, O15234
- Ligands
- ANP, MG
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, L | 5'-R(*UP*UP*UP*UP*UP*U)-3' | rna | 6 | — | — |
| A, G | Protein mago nashi homolog | protein | 144 | 36% helix, 34% strand | P61326 |
| B, H | RNA-binding protein 8A | protein | 91 | 24% helix, 35% strand | Q9Y5S9 |
| C, I | Probable ATP-dependent RNA helicase DDX48 (EC 3.6.1.-) | protein | 392 | 42% helix, 17% strand | P38919 |
| D | Protein CASC3 | protein | 56 | 25% helix, 0% strand | O15234 |
| J | Protein CASC3 | protein | 51 | 22% helix, 0% strand | O15234 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains C, I
- MG · Magnesium ion · metal · 2 copies · chains C, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.79 | 0.82 | 69 | empty |
| 2 | 667 | 0.76 | 0.81 | 70 | empty |
| 3 | 86 | 0.74 | 0.97 | 21 | empty |
| 4 | 271 | 0.73 | 0.87 | 41 | empty |
| 5 | 285 | 0.72 | 0.86 | 42 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2204 Ų buried · 44 hydrogen bonds · protein-protein
- I–J · 1948 Ų buried · 28 hydrogen bonds · protein-protein
- G–I · 1694 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 1679 Ų buried · 41 hydrogen bonds · protein-protein
- G–H · 1326 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2HYI · Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA · the same entry in another collection · chain I against I, TM-score 1.00
- Q9Y5S9 · AlphaFold monomer V2.0 prediction for RNA-binding protein 8A (Q9Y5S9) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P38919 · AlphaFold monomer V2.0 prediction for eukaryotic initiation factor 4A-III (P38919) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P61326
- Every structure of UniProt Q9Y5S9
- Every structure of UniProt P38919
- Every structure of UniProt O15234
- Elsewhere: RCSB PDB 2HYI · PDBe 2HYI · UniProt P61326 · UniProt Q9Y5S9 · UniProt P38919 · UniProt O15234
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