4S35

AMPPCP and TMP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural studies of a hyperthermophilic Thymidylate Kinase enzyme reveal conformational sub-states along the reaction coordinate

Biswas, A.Jeyakanthan, J.Sekar, K.

(2017) FEBS J 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thymidylate kinaseA, B195Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: aq_969tmk
EC: 2.7.4.9
UniProt
Find proteins for O67099 (Aquifex aeolicus (strain VF5))
Explore O67099 
Go to UniProtKB:  O67099
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACP (Subject of Investigation/LOI)
Query on ACP

Download Ideal Coordinates CCD File 
C [auth A], H [auth B]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
TMP (Subject of Investigation/LOI)
Query on TMP

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D [auth A], I [auth B]THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
 Ligand Interaction
EDO
Query on EDO

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G [auth A], M [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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L [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], J [auth B], K [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.479α = 90
b = 62.615β = 97.97
c = 73.577γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references