4D8K | pdb_00004d8k

Crystal structure of a SH3-SH2 domains of a lymphocyte-specific protein tyrosine kinase (LCK) from Homo sapiens at 2.36 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4D8K/pdb

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


• Deposited: 2012-01-10 Released: 2012-01-25 
• 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: 2.36 Å
• R-Value Free: 
  0.251 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal structure of a SH3-SH2 domains of a lymphocyte-specific protein tyrosine kinase (LCK) from Homo sapiens at 2.36 A resolution

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

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 19.87 kDa 
• Atom Count: 1,360 
• Modeled Residue Count: 163 
• Deposited Residue Count: 175 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase Lck	A	175	Homo sapiens	Mutation(s): 0  Gene Names: BC013200, LCK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P06239 (Homo sapiens) Explore P06239  Go to UniProtKB:  P06239
PHAROS:  P06239 GTEx:  ENSG00000182866

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free:  0.251 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34D8K

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.899	α = 90
b = 68.899	β = 90
c = 80.283	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
PHASER	phasing
SCALA	data scaling
PHENIX	refinement
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2012-08-29
  Changes: Structure summary
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-05-22
  Changes: Data collection