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Snapshot 3 of rig-I scanning on RNA duplex

Analyse Snapshot 3 of rig-I scanning on RNA duplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZD7
Type: protein + RNA
Length: 643 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable ATP-dependent RNA helicase DDX58; RNA duplex
EC: 3.6.4.13
UniProt: O95786
Ligands: ADP, ZN, MG
Pockets: 11 · best druggability 0.69

Structure

x-ray diffraction · 2 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	623	45% helix, 18% strand	O95786
C, D	RNA duplex	rna	10	—	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
ZN · Zinc ion · metal · chains A
MG · Magnesium ion · metal · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	776	0.69	0.76	85	empty
2	365	0.55	0.74	45	empty
3	334	0.50	0.73	28	empty
4	188	0.49	0.76	31	empty
5	57	0.41	0.81	20	empty

Interfaces

3 interfaces between chains.

A–C · 641 Å² buried · 6 hydrogen bonds · protein-nucleic
C–D · 510 Å² buried · 58 hydrogen bonds · nucleic-nucleic
A–D · 491 Å² buried · 7 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

3ZD7 · Snapshot 3 of RIG-I scanning on RNA duplex · the same entry in another collection · chain A against A, TM-score 1.00
O95786 · AlphaFold monomer V2.0 prediction for antiviral innate immune response receptor rig-I… · a predicted model of the same protein · chain A against A, TM-score 0.76

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 3ZD7 · PDBe 3ZD7 · UniProt O95786

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