MolNFT v1 · #118683 · protein + RNA
Crystal structure of rig-I helicase-rd in complex with 24-mer 5' triphosphate hairpin RNA
5F9H · Probable ATP-dependent RNA helicase DDX58: “Crystal structure of rig-I helicase-rd in complex with 24-mer 5' triphosphate hairpin RNA”. X-ray diffraction, 3 ligands (GTP, MG, ZN), 20 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 5F9H
- Type
- protein + RNA
- Length
- 4,003 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ATP-dependent RNA helicase DDX58; RNA (5'…
- EC
- 3.6.4.13
- UniProt
- O95786
- Ligands
- GTP, MG, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 646 | 43% helix, 18% strand | O95786 |
| B, D, F, H, J, L | RNA (5'- R(P*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP *C)-3') | rna | 23 | — | — |
| C | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 647 | 45% helix, 18% strand | O95786 |
| E | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 638 | 46% helix, 18% strand | O95786 |
| G | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 653 | 46% helix, 18% strand | O95786 |
| I | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 644 | 45% helix, 18% strand | O95786 |
| K | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 637 | 46% helix, 18% strand | O95786 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MG · Magnesium ion · metal · 8 copies · chains A, B, E, F, G, K, I
- ZN · Zinc ion · metal · 6 copies · chains A, C, E, G, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.85 | 0.88 | 109 | MG |
| 2 | 1197 | 0.85 | 0.86 | 84 | empty |
| 3 | 782 | 0.85 | 0.88 | 102 | empty |
| 4 | 713 | 0.83 | 0.87 | 87 | empty |
| 5 | 852 | 0.82 | 0.85 | 86 | MG |
Interfaces
14 interfaces between chains.
- I–J · 1614 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–B · 1583 Ų buried · 30 hydrogen bonds · protein-nucleic
- G–H · 1574 Ų buried · 25 hydrogen bonds · protein-nucleic
- K–L · 1544 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–E · 1521 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 5F9H · Crystal structure of RIG-I helicase-RD in complex with 24-mer 5' triphosphate hairpin RNA · 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 O95786
- Elsewhere: RCSB PDB 5F9H · PDBe 5F9H · UniProt O95786
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