4NFM | pdb_00004nfm

Human tau tubulin kinase 1 (TTBK1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.241 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4NFM

This is version 1.3 of the entry. See complete history

Literature

The structure of human tau-tubulin kinase 1 both in the apo form and in complex with an inhibitor.

Kiefer, S.E.Chang, C.J.Kimura, S.R.Gao, M.Xie, D.Zhang, Y.Zhang, G.Gill, M.B.Mastalerz, H.Thompson, L.A.Cacace, A.M.Sheriff, S.

(2014) Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 173-181

  • DOI: https://doi.org/10.1107/S2053230X14000144
  • Primary Citation Related Structures: 
    4NFM, 4NFN

  • PubMed Abstract: 

    Tau-tubulin kinase 1 (TTBK1) is a dual-specificity (serine/threonine and tyrosine) kinase belonging to the casein kinase 1 superfamily. TTBK1 is a neuron-specific kinase that regulates tau phosphorylation. Hyperphosphorylation of tau is implicated in the pathogenesis of Alzheimer's disease. Two kinase-domain constructs of TTBK1 were expressed in a baculovirus-infected insect-cell system and purified. The purified TTBK1 kinase-domain proteins were crystallized using the hanging-drop vapor-diffusion method. X-ray diffraction data were collected and the structure of TTBK1 was determined by molecular replacement both as an apo structure and in complex with a kinase inhibitor.


  • Organizational Affiliation
    • Molecular Discovery Technologies, Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA.

Macromolecule Content 

  • Total Structure Weight: 37.98 kDa 
  • Atom Count: 2,377 
  • Modeled Residue Count: 293 
  • Deposited Residue Count: 332 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tau-tubulin kinase 1332Homo sapiensMutation(s): 0 
Gene Names: TTBK1BDTKKIAA1855
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5TCY1 (Homo sapiens)
Explore Q5TCY1 
Go to UniProtKB:  Q5TCY1
PHAROS:  Q5TCY1
GTEx:  ENSG00000146216 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5TCY1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.241 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.3α = 90
b = 39.9β = 104.3
c = 50.4γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2014-02-05 
  • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2014-04-02
    Changes: Database references
  • Version 1.2: 2014-11-12
    Changes: Data collection
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description