3AFO | pdb_00003afo

Crystal Structure of Yeast NADH Kinase complexed with NADH

• PDB DOI: https://doi.org/10.2210/pdb3AFO/pdb

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


• Deposited: 2010-03-10 Released: 2011-03-16 
• Deposition Author(s): Ando, T., Ohashi, K., Ochiai, A., Miyagi, H., Kawai, S., Mikami, B., Murata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.244 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

The structural factor conferring NADH kinase activity on yeast mitochondrial Pos5

Ando, T., Ohashi, K., Ochiai, A., Miyagi, H., Kawai, S., Mikami, B., Murata, K.

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: 87.95 kDa 
• Atom Count: 6,305 
• Modeled Residue Count: 701 
• Deposited Residue Count: 776 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH kinase POS5	A, B	388	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: POS5 EC: 2.7.1.86
UniProt
Find proteins for Q06892 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06892  Go to UniProtKB:  Q06892

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	C [auth A], F [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
MPD	D [auth A], E [auth A], G [auth B], H [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.244 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.685	α = 90
b = 132.782	β = 90
c = 59.636	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-16 
Deposition Author(s): Ando, T., Ohashi, K., Ochiai, A., Miyagi, H., Kawai, S., Mikami, B., Murata, K.

Revision History  

• Version 1.0: 2011-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description