MolNFT v1 · #118674 · protein + RNA
Crystal structure of rig-I in complex with cap-0 RNA
5F98 · Probable ATP-dependent RNA helicase DDX58: “Crystal structure of rig-I in complex with cap-0 RNA”. X-ray diffraction, 3 ligands (M7G, ZN, MG), 20 pockets (best druggability 0.85). MolNFT v1 #118674 on GenesisL1: 3D structure…
- PDB
- 5F98
- Type
- protein + RNA
- Length
- 4,021 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
- M7G, ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 650 | 42% helix, 17% strand | O95786 |
| B, D, F, H, J, L | RNA (5'- R(P*GP*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 | 24 | — | — |
| C | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 648 | 43% helix, 17% strand | O95786 |
| E | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 641 | 44% helix, 17% strand | O95786 |
| G | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 647 | 44% helix, 17% strand | O95786 |
| I | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 647 | 42% helix, 16% strand | O95786 |
| K | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 644 | 43% helix, 16% strand | O95786 |
Ligands and binding sites
- M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- ZN · Zinc ion · metal · 6 copies · chains A, C, E, G, I, K
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 1164 | 0.85 | 0.86 | 75 | empty |
| 2 | 795 | 0.83 | 0.86 | 88 | MG |
| 3 | 742 | 0.83 | 0.87 | 86 | MG |
| 4 | 934 | 0.82 | 0.84 | 100 | MG |
| 5 | 710 | 0.81 | 0.86 | 74 | empty |
Interfaces
14 interfaces between chains.
- G–H · 1650 Ų buried · 30 hydrogen bonds · protein-nucleic
- K–L · 1641 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–B · 1631 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–D · 1621 Ų buried · 28 hydrogen bonds · protein-nucleic
- I–J · 1556 Ų buried · 30 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 5F98 · Crystal structure of RIG-I in complex with Cap-0 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 5F98 · PDBe 5F98 · UniProt O95786
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