Research workbench
Crystal structure of chicken MDA5 with 5'P 10-mer dsrna and ADP-MG2+ at 2.6 a resolution (monoclinic form, twinned).
Analyse Crystal structure of chicken MDA5 with 5'P 10-mer dsrna and ADP-MG2+ at 2.6 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JC3
- Type
- protein + RNA
- Length
- 1,369 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Melanoma differentiation associated protein-5; RNA…
- UniProt
- D9N195
- Ligands
- ADP, MG, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Melanoma differentiation associated protein-5 | protein | 668 | 49% helix, 16% strand | D9N195 |
| X, Y, C, D | RNA (5'-R(P*GP*GP*UP*AP*CP*GP*UP*AP*CP*C)-3') | rna | 10 | — | — |
| B | Melanoma differentiation associated protein-5 | protein | 661 | 50% helix, 16% strand | D9N195 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 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
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.86 | 0.89 | 98 | empty |
| 2 | 752 | 0.86 | 0.90 | 89 | empty |
| 3 | 1173 | 0.81 | 0.83 | 74 | empty |
| 4 | 782 | 0.81 | 0.85 | 67 | empty |
| 5 | 263 | 0.69 | 0.85 | 32 | ADP, MG |
Interfaces
9 interfaces between chains.
- A–B · 1112 Ų buried · 9 hydrogen bonds · protein-protein
- A–Y · 965 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–D · 964 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–X · 829 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–C · 822 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 5JC3 · Crystal structure of chicken MDA5 with 5'p 10-mer dsRNA and ADP-Mg2+ at 2.6 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 5JC3 · PDBe 5JC3 · UniProt D9N195
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