Research workbench
Crystal structure of chicken MDA5 with 5'P 10-mer dsrna and ADP-MG2+ at 2.95 a resolution (untwinned).
Analyse Crystal structure of chicken MDA5 with 5'P 10-mer dsrna and ADP-MG2+ at 2.95 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JCH
- Type
- protein + RNA
- Length
- 1,356 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, ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Melanoma differentiation associated protein-5 | protein | 661 | 50% helix, 17% strand | D9N195 |
| X, Y, U, V | RNA (5'-R(P*GP*GP*UP*AP*CP*GP*UP*AP*CP*C)-3') | rna | 10 | — | — |
| B | Melanoma differentiation associated protein-5 | protein | 655 | 50% helix, 16% strand | D9N195 |
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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.87 | 0.90 | 99 | empty |
| 2 | 1134 | 0.86 | 0.87 | 117 | empty |
| 3 | 986 | 0.81 | 0.83 | 64 | empty |
| 4 | 1032 | 0.80 | 0.82 | 74 | empty |
| 5 | 271 | 0.70 | 0.85 | 34 | ADP, MG |
Interfaces
9 interfaces between chains.
- B–V · 985 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–Y · 976 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–B · 924 Ų buried · 8 hydrogen bonds · protein-protein
- A–X · 814 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–U · 808 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 5JCH · Crystal structure of chicken MDA5 with 5'p 10-mer dsRNA and ADP-Mg2+ at 2.95 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 5JCH · PDBe 5JCH · UniProt D9N195
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