6G9Z

Crystal structure of human histidine triad nucleotide-binding protein 1 (hHINT1) crystallized at P212121 space group, with visible extended fragment of N-terminus

PDB DOI: https://doi.org/10.2210/pdb6G9Z/pdb
Entry: 6G9Z supersedes: 5O8G

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

Deposited: 2018-04-11 Released: 2018-04-18
Deposition Author(s): Dolot, R.M., Seda, A., Nawrot, B.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.277
R-Value Work: 0.224
R-Value Observed: 0.226

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Differences in crystal packing as the key factor for stabilization of the N-terminal fragment of hHINT1 protein

Dolot, R.M., Seda, A., Nawrot, B.C.

To be published.

Macromolecule Content

Total Structure Weight: 27.78 kDa
Atom Count: 2,408
Modelled Residue Count: 239
Deposited Residue Count: 252
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 1	A, B	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMR Query on LMR Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	(2S)-2-hydroxybutanedioic acid C₄ H₆ O₅ BJEPYKJPYRNKOW-REOHCLBHSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.277
R-Value Work: 0.224
R-Value Observed: 0.226
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.075	α = 90
b = 63.379	β = 90
c = 76.836	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-04-18

Deposition Author(s):

This entry supersedes: 5O8G

Revision History (Full details and data files)

Version 1.0: 2018-04-18
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.