3ZD7

Snapshot 3 of RIG-I scanning on RNA duplex

Structural Biology Knowledgebase: 3ZD7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.229

Literature

Macromolecules
Sequence Display for 3ZD7

Classification: HYDROLASE / RNA

Total Structure Weight: 86643.35


Macromolecule Entities
Molecule Chains Length Organism Details
PROBABLE ATP-DEPENDENT RNA HELICASE DDX58 A 696 Homo sapiens EC#: 3.6.4.13 IUBMB
Mutation: Q306N, I499S, A696L, E828D
Gene Name(s): DDX58 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
RNA DUPLEX C, D 10 Synthetic construct

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ADP
Query on ADP

A ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.229
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 48.25 α = 90.00
b = 76.00 β = 90.00
c = 207.28 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-11-25
  • Released Date: 2013-08-07
  • Deposition author(s): Luo, D., Pyle, A.M.

Revision History

  • 2013-09-11
    Type: Citation | Details: JRNL