4U1P | pdb_00004u1p

Human Fyn-SH2 domain in complex with a synthetic high-affinity phospho-peptide

• PDB DOI: https://doi.org/10.2210/pdb4U1P/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, Alphapolyomavirus mauratus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-07-16 Released: 2015-07-29 
• Deposition Author(s): Garcia-Pino, A., Huculeci, R., Lenaerts, T., van Nuland, N.A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

Human Fyn-SH2 domain in complex with a synthetic high-affinity phospho-peptide

Garcia-Pino, A., Huculeci, R., Lenaerts, T., van Nuland, N.A.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.15 kDa 
• Atom Count: 1,166 
• Modeled Residue Count: 116 
• Deposited Residue Count: 133 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase Fyn	A	122	Homo sapiens	Mutation(s): 0  Gene Names: FYN EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P06241 (Homo sapiens) Explore P06241  Go to UniProtKB:  P06241
PHAROS:  P06241 GTEx:  ENSG00000010810

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Middle T antigen	B	11	Alphapolyomavirus mauratus	Mutation(s): 0
UniProt
Find proteins for P03079 (Hamster polyomavirus) Explore P03079  Go to UniProtKB:  P03079

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
15P	C [auth A]	POLYETHYLENE GLYCOL (N=34) C69 H140 O35 VUYXVWGKCKTUMF-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.248	α = 90
b = 39.248	β = 90
c = 145.199	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): Garcia-Pino, A., Huculeci, R., Lenaerts, T., van Nuland, N.A.J.

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2018-02-07
  Changes: Database references, Source and taxonomy
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary