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Crystal structure of chicken MDA5 with 5'P 24-mer dsrna and ADP-MG2+ at 2.75 a resolution.
Analyse Crystal structure of chicken MDA5 with 5'P 24-mer dsrna and ADP-MG2+ at 2.75 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JC7
- Type
- protein + RNA
- Length
- 1,336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Melanoma differentiation associated protein-5; RNA (5'…
- UniProt
- D9N195
- Ligands
- ADP, ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Melanoma differentiation associated protein-5 | protein | 641 | 49% helix, 15% strand | D9N195 |
| B | Melanoma differentiation associated protein-5 | protein | 647 | 48% helix, 15% strand | D9N195 |
| X | RNA (5'- R(P*GP*GP*AP*CP*GP*UP*CP*AP*UP*GP*CP*GP*CP*AP*UP*GP*AP*CP*GP*UP*CP*CP *CP*C)-3') | rna | 24 | — | — |
| Y | RNA (5'- R(P*GP*GP*GP*AP*CP*GP*UP*CP*AP*UP*GP*CP*GP*CP*AP*UP*GP*AP*CP*GP*UP*CP *CP*C)-3') | rna | 24 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.87 | 0.89 | 124 | empty |
| 2 | 688 | 0.84 | 0.88 | 88 | empty |
| 3 | 244 | 0.82 | 0.95 | 35 | empty |
| 4 | 1060 | 0.81 | 0.83 | 84 | empty |
| 5 | 466 | 0.78 | 0.87 | 45 | empty |
Interfaces
6 interfaces between chains.
- X–Y · 1167 Ų buried · 112 hydrogen bonds · nucleic-nucleic
- B–X · 1067 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–B · 1042 Ų buried · 9 hydrogen bonds · protein-protein
- A–Y · 1035 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–X · 988 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 5JC7 · Crystal structure of chicken MDA5 with 5'p 24-mer dsRNA and ADP-Mg2+ at 2.75 A resolution. · the same entry in another collection · chain A against A, TM-score 1.00
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 D9N195
- Elsewhere: RCSB PDB 5JC7 · PDBe 5JC7 · UniProt D9N195
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