6YVP

Human histidine triad nucleotide-binding protein 2 (hHINT2) complexed with dGMP and refined to 2.77 A

PDB DOI: https://doi.org/10.2210/pdb6YVP/pdb

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

Deposited: 2020-04-28 Released: 2020-05-13
Deposition Author(s): Dolot, R.D., Krakowiak, A., Nawrot, B.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free: 0.308
R-Value Work: 0.208

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: 35.06 kDa
Atom Count: 1,929
Modelled Residue Count: 224
Deposited Residue Count: 326
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]	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
DGP (Subject of Investigation/LOI) Query on DGP Download Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain D [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain D [auth BBB]	C [auth AAA], D [auth BBB]	2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P LTFMZDNNPPEQNG-KVQBGUIXSA-N		Interactions Focus chain C [auth AAA] Focus chain D [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free: 0.308
R-Value Work: 0.208
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.649	α = 90
b = 36.531	β = 103.034
c = 86.887	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

Deposition Data

Released Date: 2020-05-13

Deposition Author(s):

Dolot, R.D.

Krakowiak, A.

Nawrot, B.C.

Revision History (Full details and data files)

Version 1.0: 2020-05-13
Type: Initial release
Version 1.1: 2021-11-10
Changes: Data collection, Database references
Version 1.2: 2024-01-24
Changes: Data collection, Derived calculations, Refinement description