6YI0

Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 1.65 A in P41212 space group

PDB DOI: https://doi.org/10.2210/pdb6YI0/pdb
Entry: 6YI0 supersedes: 4NJX

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

Deposited: 2020-03-31 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: 1.65 Å
R-Value Free: 0.233
R-Value Work: 0.184

wwPDB Validation 3D Report Full Report

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: 68.76 kDa
Atom Count: 3,806
Modelled Residue Count: 423
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 DDD], D [auth CCC]	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth BBB] MOL2 format, chain E [auth BBB]	E [auth BBB]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth BBB] Interactions & Density Focus chain E [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.233
R-Value Work: 0.184
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.945	α = 90
b = 76.945	β = 90
c = 140.454	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-04-29

Deposition Author(s):

This entry supersedes: 4NJX

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