3TVL

Complex between the human thiamine triphosphatase and triphosphate

• PDB DOI: https://doi.org/10.2210/pdb3TVL/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-09-20 Released: 2012-10-10 
• Deposition Author(s): Delvaux, D., Herman, R., Sauvage, E., Wins, P., Bettendorff, L., Charlier, P., Kerff, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.261 
• R-Value Work: 0.180 
• R-Value Observed: 0.184 

Literature

Structural determinants of specificity and catalytic mechanism in mammalian 25-kDa thiamine triphosphatase.

Delvaux, D., Kerff, F., Murty, M.R., Lakaye, B., Czerniecki, J., Kohn, G., Wins, P., Herman, R., Gabelica, V., Heuze, F., Tordoir, X., Maree, R., Matagne, A., Charlier, P., De Pauw, E., Bettendorff, L.

(2013) Biochim Biophys Acta 1830: 4513-4523

• PubMed: 23707715 
• DOI: https://doi.org/10.1016/j.bbagen.2013.05.014
• Primary Citation of Related Structures:  
  3TVL


• PubMed Abstract: 
  

  Thiamine triphosphate (ThTP) is present in most organisms and might be involved in intracellular signaling. In mammalian cells, the cytosolic ThTP level is controlled by a specific thiamine triphosphatase (ThTPase), belonging to the CYTH superfamily of proteins. CYTH proteins are present in all superkingdoms of life and act on various triphosphorylated substrates.

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Organizational Affiliation: 

GIGA-Neurosciences, Université de Liège, Avenue de l'Hôpital 1, Liège, Belgium.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.89 kDa 
• Atom Count: 3,308 
• Modelled Residue Count: 403 
• Deposited Residue Count: 460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamine-triphosphatase	A, B	230	Homo sapiens	Mutation(s): 0  Gene Names: THTPA EC: 3.6.1.28
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BU02 (Homo sapiens) Explore Q9BU02  Go to UniProtKB:  Q9BU02
PHAROS:  Q9BU02 GTEx:  ENSG00000259431

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3PO	C [auth A], E [auth B]	TRIPHOSPHATE H5 O10 P3 UNXRWKVEANCORM-UHFFFAOYSA-N
EDO	D [auth A], F [auth B], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3PO	PDBBind:  3TVL	Kd: 1.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.261 
• R-Value Work: 0.180 
• R-Value Observed: 0.184 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.378	α = 90
b = 63.529	β = 108.75
c = 70.95	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-10 
Deposition Author(s): Delvaux, D., Herman, R., Sauvage, E., Wins, P., Bettendorff, L., Charlier, P., Kerff, F.

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2013-06-12
  Changes: Database references
• Version 1.2: 2013-07-17
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description