3PFN | pdb_00003pfn

Crystal Structure of human NAD kinase

• PDB DOI: https://doi.org/10.2210/pdb3PFN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-10-28 Released: 2010-11-10 
• Deposition Author(s): Wang, H., Tempel, W., Wernimont, A.K., Tong, Y., Guan, X., Shen, Y., Li, Y., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.236 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Crystal Structure of human NAD kinase

Wang, H., Tempel, W., Wernimont, A.K., Tong, Y., Guan, X., Shen, Y., Li, Y., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Park, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 162.48 kDa 
• Atom Count: 9,218 
• Modeled Residue Count: 1,292 
• Deposited Residue Count: 1,460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD kinase	A, B, C, D	365	Homo sapiens	Mutation(s): 1  Gene Names: NADK EC: 2.7.1.23
UniProt & NIH Common Fund Data Resources
Find proteins for O95544 (Homo sapiens) Explore O95544  Go to UniProtKB:  O95544
PHAROS:  O95544 GTEx:  ENSG00000008130

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	AA [auth B], AB [auth C], BA [auth B], BB [auth C], CA [auth B], CB [auth C], DA [auth B], DB [auth C], E [auth A], EA [auth B], EB [auth C], F [auth A], FA [auth B], FB [auth C], G [auth A], GA [auth B], GB [auth C], H [auth A], HA [auth B], HB [auth D], I [auth A], IA [auth B], IB [auth D], J [auth A], JA [auth B], JB [auth D], K [auth A], KA [auth B], KB [auth D], L [auth A], LA [auth B], LB [auth D], M [auth A], MA [auth B], MB [auth D], N [auth A], NA [auth B], NB [auth D], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth C], Y [auth A], YA [auth C], Z [auth B], ZA [auth C]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.236 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.095	α = 90
b = 133.587	β = 90
c = 162.668	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
DM	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-10 
Deposition Author(s): Wang, H., Tempel, W., Wernimont, A.K., Tong, Y., Guan, X., Shen, Y., Li, Y., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary