Research workbench
K63-polyub MDA5CARDS complex
Analyse K63-polyub MDA5CARDS complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DNJ
- Type
- protein
- Length
- 1,369 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interferon-induced helicase C domain-containing protein 1; Ubiquitin
- EC
- 3.6.4.13
- UniProt
- Q9BYX4, P0CG47
- Pockets
- 15 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Interferon-induced helicase C domain-containing protein 1 (EC 3.6.4.13) | protein | 197 | 72% helix, 0% strand | Q9BYX4 |
| E, F, I, K | Ubiquitin | protein | 72 | 17% helix, 29% strand | P0CG47 |
| G | Ubiquitin | protein | 74 | 24% helix, 28% strand | P0CG47 |
| H, J, L | Ubiquitin | protein | 73 | 25% helix, 34% strand | P0CG47 |
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.88 | 0.90 | 114 | empty |
| 2 | 877 | 0.81 | 0.84 | 77 | empty |
| 3 | 583 | 0.73 | 0.80 | 51 | empty |
| 4 | 642 | 0.71 | 0.79 | 59 | empty |
| 5 | 606 | 0.70 | 0.79 | 44 | empty |
Interfaces
23 interfaces between chains.
- A–D · 1033 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 915 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 911 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 894 Ų buried · 12 hydrogen bonds · protein-protein
- D–G · 889 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7DNJ · K63-polyUb MDA5CARDs complex · the same entry in another collection · chain L against L, 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 Q9BYX4
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 7DNJ · PDBe 7DNJ · UniProt Q9BYX4 · UniProt P0CG47
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