4E9M

NOD1 card domain with three disulfide-clinched, domain-swapped dimers in the asymmetric unit

• PDB DOI: https://doi.org/10.2210/pdb4E9M/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-03-21 Released: 2012-04-04 
• Deposition Author(s): Berry, E.A., Huang, L.S., Walker-Kopp, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.275 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of nod1 card domain with three disulfide-clinched, domain-swapped dimers in the asymmetric unit

Berry, E.A., Huang, L.S., Walker-Kopp, N.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Biological Assembly 7  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 7 generated by PISA (software)

Biological Assembly 8  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 8 generated by PISA (software)

Biological Assembly 9  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 9 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 100.32 kDa 
• Atom Count: 4,641 
• Modelled Residue Count: 559 
• Deposited Residue Count: 864 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleotide-binding oligomerization domain-containing protein 1	A, B, C, D, E, F	144	Homo sapiens	Mutation(s): 0  Gene Names: CARD4, NOD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y239 (Homo sapiens) Explore Q9Y239  Go to UniProtKB:  Q9Y239
PHAROS:  Q9Y239 GTEx:  ENSG00000106100

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	G [auth D]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.275 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.846	α = 90
b = 85.335	β = 90
c = 113.682	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-04 
Deposition Author(s): Berry, E.A., Huang, L.S., Walker-Kopp, N.

Revision History  

• Version 1.0: 2012-04-04
  Type: Initial release
  
• Version 1.1: 2013-02-06
  Changes: Other
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-27
  Changes: Structure summary