3GA3 | pdb_00003ga3

Crystal structure of the C-terminal domain of human MDA5

• PDB DOI: https://doi.org/10.2210/pdb3GA3/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-16 Released: 2009-02-24 
• Deposition Author(s): Li, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.204 (Depositor) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the C-terminal domain of human MDA5

Li, P., Li, X., Lu, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.65 kDa 
• Atom Count: 1,296 
• Modeled Residue Count: 133 
• Deposited Residue Count: 133 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon-induced helicase C domain-containing protein 1, MDA5	A	133	Homo sapiens	Mutation(s): 0  Gene Names: IFIH1, IFIH1 or MDA5, MDA5, RH116 EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYX4 (Homo sapiens) Explore Q9BYX4  Go to UniProtKB:  Q9BYX4
PHAROS:  Q9BYX4 GTEx:  ENSG00000115267

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.204 (Depositor) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.41	α = 90
b = 60.92	β = 102.58
c = 36.443	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-24 
Deposition Author(s): Li, P.

Revision History  

• Version 1.0: 2009-02-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-04-03
  Changes: Refinement description