6YPX

Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 2.11 A in C2221 space group

PDB DOI: https://doi.org/10.2210/pdb6YPX/pdb
Entry: 6YPX supersedes: 4NJZ

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

Deposited: 2020-04-16 Released: 2020-04-29
Deposition Author(s): Dolot, R.D., Wlodarczyk, A., Bujacz, G.D., Nawrot, B.C.
Funding Organization(s): Ministry of Science and Higher Education (Poland)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.184
R-Value Work: 0.148

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Biochemical, crystallographic and biophysical characterization of histidine triad nucleotide-binding protein 2 with different ligands including a non-hydrolyzable analog of Ap4A.

Dolot, R., Krakowiak, A., Kaczmarek, R., Wlodarczyk, A., Pichlak, M., Nawrot, B.

(2021) Biochim Biophys Acta Gen Subj 1865: 129968-129968

PubMed: 34329705 Search on PubMed
DOI: https://doi.org/10.1016/j.bbagen.2021.129968
Primary Citation of Related Structures:
6YI0, 6YPR, 6YPX, 6YQD, 6YQM, 6YVP

PubMed Abstract:
Human HINT2 is an important mitochondrial enzyme involved in many processes such as apoptosis and bioenergetics, but its endogenous substrates and the three-dimensional structure of the full-length protein have not been identified yet.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 69.24 kDa
Atom Count: 4,339
Modelled Residue Count: 452
Deposited Residue Count: 652
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine triad nucleotide-binding protein 2, mitochondrial	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	163	Homo sapiens	Mutation(s): 0 Gene Names: HINT2 EC: 3
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BX68
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAC (Subject of Investigation/LOI) Query on CAC Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain I [auth DDD] MOL2 format, chain E [auth AAA] MOL2 format, chain I [auth DDD]	E [auth AAA], I [auth DDD]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain E [auth AAA] Focus chain I [auth DDD] Interactions & Density Focus chain E [auth AAA] Focus chain I [auth DDD]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth BBB] SDF format, chain G [auth CCC] MOL2 format, chain F [auth BBB] MOL2 format, chain G [auth CCC]	F [auth BBB], G [auth CCC]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth BBB] Focus chain G [auth CCC] Interactions & Density Focus chain F [auth BBB] Focus chain G [auth CCC]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth CCC] SDF format, chain J [auth DDD] MOL2 format, chain H [auth CCC] MOL2 format, chain J [auth DDD]	H [auth CCC], J [auth DDD]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth CCC] Focus chain J [auth DDD] Interactions & Density Focus chain H [auth CCC] Focus chain J [auth DDD]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.184
R-Value Work: 0.148
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.411	α = 90
b = 153.992	β = 90
c = 74.785	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-04-29

Deposition Author(s):

This entry supersedes: 4NJZ

Funding Organization	Location	Grant Number
Ministry of Science and Higher Education (Poland)	Poland	N N204 516139

Revision History (Full details and data files)

Version 1.0: 2020-04-29
Type: Initial release
Version 1.1: 2021-11-10
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2024-01-24
Changes: Data collection, Derived calculations, Refinement description