4ZKL

Crystal structure of human histidine triad nucleotide-binding protein 1 (hHINT1) complexed with JB419 (AP4A analog)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystallographic studies of the complex of human HINT1 protein with a non-hydrolyzable analog of Ap4A.

Dolot, R., Kaczmarek, R., Seda, A., Krakowiak, A., Baraniak, J., Nawrot, B.

(2016) Int.J.Biol.Macromol. 87: 62-69

  • DOI: 10.1016/j.ijbiomac.2016.02.047
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Histidine triad nucleotide-binding protein 1 (HINT1) represents the most ancient and widespread branch in the histidine triad proteins superfamily. HINT1 plays an important role in various biological processes, and it has been found in many species. ...

    Histidine triad nucleotide-binding protein 1 (HINT1) represents the most ancient and widespread branch in the histidine triad proteins superfamily. HINT1 plays an important role in various biological processes, and it has been found in many species. Here, we report the first structure (at a 2.34Å resolution) of a complex of human HINT1 with a non-hydrolyzable analog of an Ap4A dinucleotide, containing bis-phosphorothioated glycerol mimicking a polyphosphate chain, obtained from a primitive monoclinic space group P21 crystal. In addition, the apo form of hHINT1 at the space group P21 refined to 1.92Å is reported for comparative studies.

    Organizational Affiliation: 

    Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland. Electronic address: rdolot@cbmm.lodz.pl.,Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histidine triad nucleotide-binding protein 1
A, B, C, D
126Homo sapiensMutation(s): 0 
Gene Names: HINT1 (HINT, PKCI1, PRKCNH1)
EC: 3.-.-.-
Find proteins for P49773 (Homo sapiens)
Go to Gene View: HINT1
Go to UniProtKB:  P49773
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JB6
Query on JB6
Download SDF File 
Download CCD File 
B
(2R,3R,4S,5R)-2-(6-aminopurin-9-yl)-5-[2-[[(2S)-3-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-2-oxidanyl-propoxy]-sulfanyl-phosphoryl]oxyethyl]oxolane-3,4-diol
C24 H34 N10 O13 P2 S2
OABPMBSLNAAXBR-CZUYOEIMSA-N
 Ligand Interaction
AMP
Query on AMP
Download SDF File 
Download CCD File 
B, D
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.714α = 90.00
b = 46.419β = 97.41
c = 103.413γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
REFMACrefinement
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-09
    Type: Database references
  • Version 1.2: 2018-03-07
    Type: Data collection