2UYY

Structure of the cytokine-like nuclear factor n-pac

• PDB DOI: https://doi.org/10.2210/pdb2UYY/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-04-20 Released: 2007-07-03 
• Deposition Author(s): Tickle, J., Pilka, E.S., Bunkoczi, G., Berridge, G., Smee, C., Kavanagh, K.L., Hozjan, V., Niesen, F.H., Papagrigoriou, E., Pike, A.C.W., Turnbull, A., Arrowsmith, C.H., Edwards, A., Sundstrom, M., Weigelt, J., von Delft, F., Oppermann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Models: experimental

Literature

The Structure of the Cytokine-Like Nuclear Factor N-Pac

Tickle, J., Pilka, E.S., Bunkoczi, G., Berridge, G., Smee, C., Kavanagh, K.L., Hozjan, V., Niesen, F.H., Papagrigoriou, E., Pike, A.C.W., Turnbull, A., Arrowsmith, C.H., Edwards, A., Sundstrom, M., Weigelt, J., von Delft, F., Oppermann, U.

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 PQS (software)

Macromolecule Content

• Total Structure Weight: 137.75 kDa 
• Atom Count: 9,183 
• Modelled Residue Count: 1,167 
• Deposited Residue Count: 1,264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-PAC PROTEIN	A, B, C, D	316	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q49A26 (Homo sapiens) Explore Q49A26  Go to UniProtKB:  Q49A26
PHAROS:  Q49A26 GTEx:  ENSG00000140632

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA7	F [auth A], J [auth D]	[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE C15 H24 N5 O16 P3 XDDBFIXGEVGCEU-AOOZFPJJSA-N
K	E [auth A], G [auth B], H [auth C], I [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.18	α = 90
b = 134.18	β = 90
c = 261.463	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-03 
Deposition Author(s): Tickle, J., Pilka, E.S., Bunkoczi, G., Berridge, G., Smee, C., Kavanagh, K.L., Hozjan, V., Niesen, F.H., Papagrigoriou, E., Pike, A.C.W., Turnbull, A., Arrowsmith, C.H., Edwards, A., Sundstrom, M., Weigelt, J., von Delft, F., Oppermann, U.

Revision History  

• Version 1.0: 2007-07-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.3: 2018-02-28
  Changes: Source and taxonomy
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description