4INI

Human Histidine Triad Nucleotide Binding Protein 2 with Bound AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural characterization of human histidine triad nucleotide-binding protein 2, a member of the histidine triad superfamily.

Maize, K.M.Wagner, C.R.Finzel, B.C.

(2013) FEBS J 280: 3389-3398

  • DOI: https://doi.org/10.1111/febs.12330
  • Primary Citation of Related Structures:  
    4INC, 4INI

  • PubMed Abstract: 

    The histidine triad proteins (HITs) constitute a large and ubiquitous superfamily of nucleotide hydrolases. The human histidine triad nucleotide-binding proteins (hHints) are a distinct class of HITs noted for their acyl-AMP hydrolase and phosphoramidase activity. The first high-resolution crystal structures of hHint2 with and without bound AMP are described. The differences between hHint2 and previously known HIT family protein structures are discussed. HIT family enzymes have historically been divided into five classes based on their catalytic specificity: Hint, fragile HIT protein, galactose-1-phosphate uridylyltransferase, DcpS and aprataxin. However, although several structures exist for the enzymes in these classes, the endogenous substrates of many of these enzymes have not been identified or biochemically characterized. To better understand the structural relationships of the HIT enzymes, a structure-based phylogeny was constructed that resulted in the identification of several new putative HIT clades with potential acyl-AMP hydrolase and phosphoramidase activity.


  • Organizational Affiliation

    Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histidine triad nucleotide-binding protein 2, mitochondrial
A, B
130Homo sapiensMutation(s): 0 
Gene Names: HINT2
EC: 3 (PDB Primary Data), 3.9.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BX68 (Homo sapiens)
Explore Q9BX68 
Go to UniProtKB:  Q9BX68
PHAROS:  Q9BX68
GTEx:  ENSG00000137133 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BX68
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
D [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG5
Query on PG5

Download Ideal Coordinates CCD File 
G [auth B]1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
C8 H18 O4
YFNKIDBQEZZDLK-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.572α = 90
b = 72.77β = 90
c = 77.724γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description