MolNFT v1 · #85139 · protein + RNA
Structure of duck rig-I helicase domain bound to 19-mer dsrna and ATP transition state analogue
4A36 · Retinoic acid inducible protein I: “Structure of duck rig-I helicase domain bound to 19-mer dsrna and ATP transition state analogue”. X-ray diffraction, 3 ligands (ADP, AF3, MG), 19 pockets (best druggability 0.81). MolNFT v1 #85139…
- PDB
- 4A36
- Type
- protein + RNA
- Length
- 1,120 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid inducible protein I; 5'-R(*GP*CP*AP*UP*GP*CP*GP*AP*CP*CP*UP*CP*UP*GP…
- UniProt
- D3TI84
- Ligands
- ADP, AF3, MG
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid inducible protein I | protein | 523 | 54% helix, 11% strand | D3TI84 |
| B | Retinoic acid inducible protein I | protein | 523 | 52% helix, 10% strand | D3TI84 |
| R | 5'-R(*GP*CP*AP*UP*GP*CP*GP*AP*CP*CP*UP*CP*UP*GP *UP*UP*UP*GP*A)-3' | rna | 19 | — | — |
| S | 5'-R(*UP*CP*AP*AP*AP*CP*AP*GP*AP*GP*GP*UP*CP*GP *CP*AP*UP*GP*C)-3' | rna | 19 | — | — |
| T | 5'-R(*GP*CP*AP*UP*GP*CP*GP*AP*CP*CP*UP*CP*UP*GP *UP*UP*UP*GP*A)-3' | rna | 18 | — | — |
| U | 5'-R(*UP*CP*AP*AP*AP*CP*AP*GP*AP*GP*GP*UP*CP*GP *CP*AP*UP*GP*C)-3' | rna | 18 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- AF3 · Aluminum fluoride · ligand · 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
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.81 | 0.82 | 81 | empty |
| 2 | 1087 | 0.80 | 0.81 | 88 | empty |
| 3 | 378 | 0.64 | 0.79 | 39 | ADP, MG, AF3 |
| 4 | 646 | 0.63 | 0.75 | 35 | empty |
| 5 | 323 | 0.61 | 0.78 | 30 | empty |
Interfaces
11 interfaces between chains.
- T–U · 898 Ų buried · 87 hydrogen bonds · nucleic-nucleic
- R–S · 897 Ų buried · 82 hydrogen bonds · nucleic-nucleic
- B–U · 771 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–S · 767 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–R · 369 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 4A36 · Structure of duck RIG-I helicase domain bound to 19-mer dsRNA and ATP transition state… · 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 D3TI84
- Elsewhere: RCSB PDB 4A36 · PDBe 4A36 · UniProt D3TI84
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