3TW2

High resolution structure of human histidine triad nucleotide-binding protein 1 (hHINT1)/AMP complex in a monoclinic space group

• PDB DOI: https://doi.org/10.2210/pdb3TW2/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-09-21 Released: 2011-11-02 
• Deposition Author(s): Dolot, R.M., Wlodarczyk, A., Ozga, M., Krakowiak, A., Nawrot, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 0.161 
• R-Value Work: 0.121 
• R-Value Observed: 0.123 

Starting Model: experimental

Literature

A new crystal form of human histidine triad nucleotide-binding protein 1 (hHINT1) in complex with adenosine 5'-monophosphate at 1.38 A resolution.

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

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 883-888

• PubMed: 22869114 
• DOI: https://doi.org/10.1107/S1744309112029491
• Primary Citation of Related Structures:  
  3TW2


• PubMed Abstract: 
  

  Histidine triad nucleotide-binding protein 1 (HINT1) represents the most ancient and widespread branch of the histidine triad protein superfamily. HINT1 plays an important role in various biological processes and has been found in many species. Here, the structure of the human HINT1-adenosine 5'-monophosphate (AMP) complex at 1.38 Å resolution obtained from a new monoclinic crystal form is reported. The final structure has R(cryst) = 0.1207 (R(free) = 0.1615) and the model exhibits good stereochemical quality. Detailed analysis of the high-resolution data allowed the details of the protein structure to be updated in comparison to the previously published data.

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Organizational Affiliation: 

Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, 90-363 Łódź, Poland. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 28 kDa 
• Atom Count: 2,482 
• Modelled Residue Count: 228 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine triad nucleotide-binding protein 1	A, B	126	Homo sapiens	Mutation(s): 0  Gene Names: HINT1, HINT, PKCI1, PRKCNH1 EC: 3 (PDB Primary Data), 3.4.22 (UniProt), 3.9.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49773 (Homo sapiens) Explore P49773  Go to UniProtKB:  P49773
PHAROS:  P49773 GTEx:  ENSG00000169567

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 0.161 
• R-Value Work: 0.121 
• R-Value Observed: 0.123 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.421	α = 90
b = 46.449	β = 94.42
c = 64.034	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-02 
Deposition Author(s): Dolot, R.M., Wlodarczyk, A., Ozga, M., Krakowiak, A., Nawrot, B.

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release
  
• Version 1.1: 2012-08-08
  Changes: Database references
• Version 1.2: 2013-01-23
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description