5UKD | pdb_00005ukd

PH INFLUENCES FLUORIDE COORDINATION NUMBER OF THE ALFX PHOSPHORYL TRANSFER TRANSITION STATE ANALOG

• PDB DOI: https://doi.org/10.2210/pdb5UKD/pdb

• Classification: TRANSFERASE
• Organism(s): Dictyostelium discoideum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-04-18 Released: 1999-08-14 
• Deposition Author(s): Schlichting, I., Reinstein, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.241 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

pH influences fluoride coordination number of the AlFx phosphoryl transfer transition state analog.

Schlichting, I., Reinstein, J.

(1999) Nat Struct Biol 6: 721-723

• PubMed: 10426946 
• DOI: https://doi.org/10.1038/11485
• Primary Citation Related Structures: 
  1QF9, 5UKD

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Organizational Affiliation: 
• Max Planck Institut für Molekulare Physiologie, Abteilung Physikalische Biochemie, Otto-Hahn-Strasse 11, Postfach 500247, D-44227, Dortmund, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.83 kDa 
• Atom Count: 1,771 
• Modeled Residue Count: 194 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE	A	194	Dictyostelium discoideum	Mutation(s): 0  Gene Names: KCY_DICDI EC: 2.7.4.14
UniProt
Find proteins for P20425 (Dictyostelium discoideum) Explore P20425  Go to UniProtKB:  P20425

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
C5P	D [auth A]	CYTIDINE-5'-MONOPHOSPHATE C9 H14 N3 O8 P IERHLVCPSMICTF-XVFCMESISA-N
AF3	E [auth A]	ALUMINUM FLUORIDE Al F3 KLZUFWVZNOTSEM-UHFFFAOYSA-K
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.241 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.209 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.5	α = 90
b = 77.5	β = 90
c = 100.2	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
XSCALE	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-08-14 
Deposition Author(s): Schlichting, I., Reinstein, J.

Revision History  

• Version 1.0: 1999-08-14
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-02-12
  Changes: Refinement description
• Version 1.4: 2017-10-04
  Changes: Refinement description
• Version 1.5: 2019-11-27
  Changes: Database references
• Version 1.6: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description