Research workbench
Structural basis for dsrna duplex backbone recognition by MDA5
Analyse Structural basis for dsrna duplex backbone recognition by MDA5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GL2
- Type
- protein + RNA
- Length
- 1,280 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interferon-induced helicase C domain-containing protein 1; RNA…
- EC
- 3.6.4.13
- UniProt
- Q9BYX4
- Ligands
- ANP, ZN
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interferon-induced helicase C domain-containing protein 1 (EC 3.6.4.13) | protein | 617 | 47% helix, 15% strand | Q9BYX4 |
| B | Interferon-induced helicase C domain-containing protein 1 (EC 3.6.4.13) | protein | 615 | 50% helix, 13% strand | Q9BYX4 |
| C, E | RNA (5'-R(*AP*UP*CP*CP*GP*CP*GP*GP*CP*CP*CP*U)-3') | rna | 12 | — | — |
| F, D | RNA (5'-R(P*AP*GP*GP*GP*CP*CP*GP*CP*GP*GP*AP*U)-3') | rna | 12 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.84 | 0.88 | 82 | empty |
| 2 | 367 | 0.80 | 0.90 | 51 | empty |
| 3 | 608 | 0.79 | 0.85 | 75 | ANP |
| 4 | 927 | 0.77 | 0.80 | 58 | empty |
| 5 | 846 | 0.76 | 0.80 | 72 | empty |
Interfaces
7 interfaces between chains.
- B–F · 1119 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–D · 1093 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–E · 880 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 853 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–B · 708 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4GL2 · Structural Basis for dsRNA duplex backbone recognition by MDA5 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9BYX4 · AlphaFold monomer V2.0 prediction for interferon-induced helicase C domain-containing… · a predicted model of the same protein · chain B 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 Q9BYX4
- Elsewhere: RCSB PDB 4GL2 · PDBe 4GL2 · UniProt Q9BYX4
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