4K11 | pdb_00004k11

The structure of 1NA in complex with Src T338G

• PDB DOI: https://doi.org/10.2210/pdb4K11/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2013-04-04 Released: 2014-04-09 
• Deposition Author(s): Eck, M.J., Yun, C.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

The structure of 1NA in complex with Src T338G

Eck, M.J., Yun, C.H.

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: 51.53 kDa 
• Atom Count: 3,908 
• Modeled Residue Count: 448 
• Deposited Residue Count: 448 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A	448	Homo sapiens	Mutation(s): 1  Gene Names: SRC, SRC1 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P12931 (Homo sapiens) Explore P12931  Go to UniProtKB:  P12931
PHAROS:  P12931 GTEx:  ENSG00000197122

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0J9	B [auth A]	1-tert-butyl-3-(naphthalen-1-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine C19 H19 N5 XSHQBIXMLULFEV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
0J9	BindingDB:  4K11	IC50: min: 340, max: 1300 (nM) from 2 assay(s)
PTR	BindingDB:  4K11	-TΔS: -1.81e+1 (kJ/mol) from 1 assay(s)
		ΔG: -2.14e+1 (kJ/mol) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.96	α = 90
b = 72.72	β = 90
c = 171.98	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-09 
Deposition Author(s): Eck, M.J., Yun, C.H.

Revision History  

• Version 1.0: 2014-04-09
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-12-06
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Structure summary