3QGZ

Re-investigated high resolution crystal structure of histidine triad nucleotide-binding protein 1 (HINT1) from rabbit complexed with adenosine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

Starting Model: experimental
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Literature

High-resolution X-ray crystal structure of rabbit histidine triad nucleotide-binding protein 1 (rHINT1) - adenosine complex at 1.10A resolution

Dolot, R., Ozga, M., Krakowiak, A., Nawrot, B.

(2011) Acta Crystallogr D Biol Crystallogr 67: 601-607

  • DOI: https://doi.org/10.1107/S0907444911015605
  • Primary Citation of Related Structures:  
    3QGZ

  • PubMed Abstract: 

    Histidine triad nucleotide-binding protein 1 (HINT1) represents the most ancient and widespread branch in the histidine-triad protein superfamily. HINT1 plays an important role in various biological processes and has been found in many species. Here, the first complete structure of the rabbit HINT1-adenosine complex is reported at 1.10 Å resolution, which is one of the highest resolutions obtained for a HINT1 structure. The final structure has an R(cryst) of 14.25% (R(free) = 16.77%) and the model exhibits good stereochemical qualities. A detailed analysis of the atomic resolution data allowed an update of the details of the protein structure in comparison to previously published data.

    • Organizational Affiliation: 

    Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies of the Polish Academy of Sciences, Łódź, Poland. [email protected]


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histidine triad nucleotide-binding protein 1126Oryctolagus cuniculusMutation(s): 0 
Gene Names: HINT1, HINT
EC: 3 (PDB Primary Data), 3.4.22 (UniProt), 3.9.1 (UniProt)
UniProt
Find proteins for P80912 (Oryctolagus cuniculus)
Explore P80912 
Go to UniProtKB:  P80912
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80912
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADN
Query on ADN
Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.747α = 90
b = 39.747β = 90
c = 141.83γ = 90
Software Package:
Software NamePurpose
MAR345data collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-10-26
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description