4ZKL

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

PDB DOI: https://doi.org/10.2210/pdb4ZKL/pdb

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

Deposited: 2015-04-30 Released: 2016-03-02
Deposition Author(s): Dolot, R.M., Kaczmarek, R., Seda, A., Krakowiak, A., Baraniak, J., Nawrot, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.239
R-Value Work: 0.186
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 26905466 Search on PubMed
DOI: https://doi.org/10.1016/j.ijbiomac.2016.02.047
Primary Citation of Related Structures:
4ZKL, 4ZKV

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. 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.

Macromolecule Content

Total Structure Weight: 56.79 kDa
Atom Count: 3,803
Modelled Residue Count: 451
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine triad nucleotide-binding protein 1	A, B, C, D	126	Homo sapiens	Mutation(s): 0 Gene Names: HINT1, HINT, PKCI1, PRKCNH1 EC: 3
UniProt & NIH Common Fund Data Resources
Find proteins for P49773 (Homo sapiens) Explore P49773 Go to UniProtKB: P49773
PHAROS: P49773 GTEx: ENSG00000169567
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49773
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JB6 Query on JB6 Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B]	F [auth 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		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain G [auth D] MOL2 format, chain E [auth B] MOL2 format, chain G [auth D]	E [auth B], G [auth D]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain E [auth B] Focus chain G [auth D] Interactions & Density Focus chain E [auth B] Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.239
R-Value Work: 0.186
R-Value Observed: 0.189
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.714	α = 90
b = 46.419	β = 97.41
c = 103.413	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-03-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-03-02
Type: Initial release
Version 1.1: 2016-03-09
Changes: Database references
Version 1.2: 2018-03-07
Changes: Data collection
Version 1.3: 2024-01-10
Changes: Data collection, Database references, Refinement description