5CM7

Structure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with adenosine diphosphate (ADP) and thiamine diphosphate (TPP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.142 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Crystal structures of thiamine monophosphate kinase from Acinetobacter baumannii in complex with substrates and products.

Sullivan, A.H.Dranow, D.M.Horanyi, P.S.Lorimer, D.D.Edwards, T.E.Abendroth, J.

(2019) Sci Rep 9: 4392-4392

  • DOI: https://doi.org/10.1038/s41598-019-40558-x
  • Primary Citation of Related Structures:  
    5CC8, 5CM7, 5DD7, 6MFM

  • PubMed Abstract: 

    Thiamine monophosphate kinase (ThiL) catalyzes the last step of thiamine pyrophosphate (TPP) synthesis, the ATP-dependent phosphorylation of thiamine monophosphate (TMP) to thiamine pyrophosphate. We solved the structure of ThiL from the human pathogen A. baumanii in complex with a pair of substrates TMP and a non-hydrolyzable adenosine triphosphate analog, and in complex with a pair of products TPP and adenosine diphosphate. High resolution of the data and anomalous diffraction allows for a detailed description of the binding mode of substrates and products, and their metal environment. The structures further support a previously proposed in-line attack reaction mechanism and show a distinct variability of metal content of the active site.


  • Organizational Affiliation

    UCB/Beryllium Discovery, 98110, 7869 NE Day Road West, Bainbridge Island, WA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thiamine-monophosphate kinase
A, B
313Acinetobacter baumanniiMutation(s): 0 
Gene Names: thiLABUW_0092
EC: 2.7.4.16
UniProt
Find proteins for A0A0D5YC82 (Acinetobacter baumannii)
Explore A0A0D5YC82 
Go to UniProtKB:  A0A0D5YC82
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0D5YC82
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A],
O [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
TPP
Query on TPP

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]
H [auth A]
I [auth A]
L [auth B]
M [auth B]
D [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
P [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
J [auth A],
N [auth B],
Q [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A],
R [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.75α = 90
b = 117.12β = 108.57
c = 55.89γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description