3RKU | pdb_00003rku

Substrate Fingerprint and the Structure of NADP+ Dependent Serine Dehydrogenase from Saccharomyces cerevisiae complexed with NADP+

• PDB DOI: https://doi.org/10.2210/pdb3RKU/pdb

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


• Deposited: 2011-04-18 Released: 2011-06-01 
• Deposition Author(s): Huether, R., Pacheco, C.M., Duax, W.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.245 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Substrate Fingerprint and the Structure of NADP+ Dependent Serine Dehydrogenase from Saccharomyces cerevisiae complexed with NADP+

Huether, R., Pacheco, C.M., Duax, W.L.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 128.79 kDa 
• Atom Count: 9,004 
• Modeled Residue Count: 1,072 
• Deposited Residue Count: 1,148 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase YMR226C	A, B, C, D	287	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: YM9959.08C, YMR226C EC: 1 (PDB Primary Data), 1.1.1.381 (UniProt), 1.1.1 (UniProt)
UniProt
Find proteins for Q05016 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05016  Go to UniProtKB:  Q05016

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], F [auth B], G [auth C], H [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.245 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.39	α = 90
b = 87.25	β = 112.98
c = 83.81	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-01 
Deposition Author(s): Huether, R., Pacheco, C.M., Duax, W.L.

Revision History  

• Version 1.0: 2011-06-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description