4E6R

Crystal structure of a Cytoplasmic protein NCK2 (NCK2) from Homo sapiens at 2.20 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4E6R/pdb

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


• Deposited: 2012-03-15 Released: 2012-04-04 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.227 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 

Literature

Crystal structure of a Cytoplasmic protein NCK2 (NCK2) from Homo sapiens at 2.20 A resolution

Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 14.02 kDa 
• Atom Count: 1,033 
• Modelled Residue Count: 116 
• Deposited Residue Count: 116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytoplasmic protein NCK2	A, B	58	Homo sapiens	Mutation(s): 0  Gene Names: BC007195, GRB4, NCK2
UniProt & NIH Common Fund Data Resources
Find proteins for O43639 (Homo sapiens) Explore O43639  Go to UniProtKB:  O43639
PHAROS:  O43639 GTEx:  ENSG00000071051

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	F [auth A], I [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	C [auth A], D [auth A], E [auth A], G [auth A], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNL	H [auth A], J [auth B]	Unknown ligand PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A, B	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.227 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 
• Space Group: P 6₅ 2 2
• Diffraction Data: https://doi.org/10.18430/M34E6R

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.398	α = 90
b = 108.398	β = 90
c = 68.199	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-04 
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

Revision History  

• Version 1.0: 2012-04-04
  Type: Initial release
  
• Version 1.1: 2015-10-21
  Changes: Database references, Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations