2VKN | pdb_00002vkn

YEAST SHO1 SH3 DOMAIN COMPLEXED WITH A PEPTIDE FROM PBS2

• PDB DOI: https://doi.org/10.2210/pdb2VKN/pdb
• Entry: 2VKN supersedes: 2QK6

• Classification: MEMBRANE PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-12-20 Released: 2008-02-05 
• Deposition Author(s): Kursula, P., Kursula, I., Song, Y.H., Paraskevopoulos, K., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.238 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Structural Genomics of Yeast SH3 Domains

Kursula, P., Kursula, I., Pinotsis, N., Song, Y.H., Lehmann, F., Zou, P., Wilmanns, M.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 9.7 kDa 
• Atom Count: 665 
• Modeled Residue Count: 75 
• Deposited Residue Count: 82 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN SSU81	A	70	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40073 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40073  Go to UniProtKB:  P40073

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MAP KINASE KINASE PBS2	B [auth C]	12	Saccharomyces cerevisiae	Mutation(s): 0  EC: 2.7.12.2
UniProt
Find proteins for P08018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P08018  Go to UniProtKB:  P08018

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth C], E [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.238 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.49	α = 90
b = 67.49	β = 90
c = 33.17	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-05 
Deposition Author(s): Kursula, P., Kursula, I., Song, Y.H., Paraskevopoulos, K., Wilmanns, M.
• This entry supersedes: 2QK6

Revision History  

• Version 1.0: 2008-02-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2019-01-30
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description