5UKD

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.241
R-Value Work: 0.209

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1038/11485
Primary Citation of Related Structures:
1QF9, 5UKD

Organizational Affiliation

Max Planck Institut für Molekulare Physiologie, Abteilung Physikalische Biochemie, Otto-Hahn-Strasse 11, Postfach 500247, D-44227, Dortmund, Germany. joachim.reinstein@mpi-dortmund.mpg.de

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20425
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
C5P Query on C5P Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CYTIDINE-5'-MONOPHOSPHATE C₉ H₁₄ N₃ O₈ P IERHLVCPSMICTF-XVFCMESISA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
AF3 Query on AF3 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ALUMINUM FLUORIDE Al F₃ KLZUFWVZNOTSEM-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.241
R-Value Work: 0.209
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1999-08-14

Deposition Author(s):

Schlichting, I.

Reinstein, J.

Revision History (Full details and data files)

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