4IKM

X-ray structure of CARD8 CARD domain

• PDB DOI: https://doi.org/10.2210/pdb4IKM/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Escherichia coli K-12, Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-12-26 Released: 2013-05-08 
• Deposition Author(s): Jin, T., Huang, M., Smith, P., Jiang, J., Xiao, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.253 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

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: 54.09 kDa 
• Atom Count: 3,703 
• Modelled Residue Count: 463 
• Deposited Residue Count: 469 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein, Caspase recruitment domain-containing protein 8	A	469	Escherichia coli K-12, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: b4034, CARD8, TUCAN, CARDINAL, JW3994, malE, KIAA0955, NDPP1
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for Q9Y2G2 (Homo sapiens) Explore Q9Y2G2  Go to UniProtKB:  Q9Y2G2
PHAROS:  Q9Y2G2 GTEx:  ENSG00000105483
UniProt Groups	Q9Y2G2P0AEX9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	C [auth A], D [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
IYR	A	L-PEPTIDE LINKING	C9 H10 I N O3		TYR
TYI	A	L-PEPTIDE LINKING	C9 H9 I2 N O3		TYR

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.253 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.877	α = 90
b = 94.877	β = 90
c = 219.39	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Jin, T., Huang, M., Smith, P., Jiang, J., Xiao, T.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2013-06-05
  Changes: Database references
• Version 1.2: 2017-08-02
  Changes: Advisory, Refinement description, Source and taxonomy
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-20
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary