MolNFT v1 · #123187 · protein + RNA
Crystal structure of chicken MDA5 with 5'P 10-mer dsrna and ADP-MG2+ at 2.6 a resolution (orthorhombic form).
5JCF · Melanoma differentiation associated protein-5: “Crystal structure of chicken MDA5 with 5'P 10-mer dsrna and ADP-MG2+ at 2.6 a resolution (orthorhombic form).”. X-ray diffraction, 3 ligands (ADP, MG, ZN), 20 pockets (best…
- PDB
- 5JCF
- Type
- protein + RNA
- Length
- 1,361 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 0.87
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Melanoma differentiation associated protein-5 | protein | 660 | 49% helix, 16% strand | D9N195 |
| X, C, D | RNA (5'-R(P*GP*GP*UP*AP*CP*GP*UP*AP*CP*C)-3') | rna | 10 | — | — |
| Y | RNA (5'-R(P*AP*GP*GP*UP*AP*CP*GP*UP*AP*CP*C)-3') | rna | 11 | — | — |
| B | Melanoma differentiation associated protein-5 | protein | 660 | 49% 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 803 | 0.87 | 0.90 | 96 | empty |
| 2 | 849 | 0.86 | 0.89 | 97 | empty |
| 3 | 639 | 0.79 | 0.84 | 54 | empty |
| 4 | 416 | 0.77 | 0.87 | 41 | empty |
| 5 | 277 | 0.67 | 0.83 | 32 | ADP, MG |
Interfaces
11 interfaces between chains.
- A–B · 1035 Ų buried · 9 hydrogen bonds · protein-protein
- A–Y · 960 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–D · 951 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–C · 823 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–X · 821 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 5JCF · 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 5JCF · PDBe 5JCF · UniProt D9N195
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