6XNE | pdb_00006xne

GCN4-p1 Peptide Trimer with p-methylphenylalanine residue at position 16 (me-F16)

• PDB DOI: https://doi.org/10.2210/pdb6XNE/pdb

• Classification: TRANSCRIPTION
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 2020-07-02 Released: 2021-07-07 
• Deposition Author(s): Rowe Hartje, R.K., Czarny, R.S., Ho, A.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.309 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Engineering Specific Protein-Protein Interactions Through Halogen and Hydrogen Bonds

Rowe Hartje, R.K., Ferrero, M., Cavallo, G., Metrangolo, P., Ho, A., Czarny, R., Ho, P.S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 11.11 kDa 
• Atom Count: 884 
• Modeled Residue Count: 90 
• Deposited Residue Count: 90 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GCN4-p1 Peptide with me-F16	A	30	Saccharomyces cerevisiae	Mutation(s): 1
UniProt
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P03069  Go to UniProtKB:  P03069

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GCN4-p1 Peptide with A16	B, C	30	Saccharomyces cerevisiae	Mutation(s): 1
UniProt
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P03069  Go to UniProtKB:  P03069

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	D [auth A], E [auth A], F [auth A], G [auth B], H [auth C], I [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4PH	A	L-PEPTIDE LINKING	C10 H13 N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.309 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.138	α = 90
b = 34.891	β = 100.628
c = 47.041	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-07 
Deposition Author(s): Rowe Hartje, R.K., Czarny, R.S., Ho, A.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1608146
National Science Foundation (NSF, United States)	United States	1905328

Revision History  

• Version 1.0: 2021-07-07
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary