5O8I | pdb_00005o8i

Crystal structure of human histidine triad nucleotide-binding protein 1 (hHINT1) crystallized at P212121 space group, and refined to 1.27 A

PDB DOI: https://doi.org/10.2210/pdb5O8I/pdb

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

Deposited: 2017-06-13 Released: 2017-06-28
Deposition Author(s): Dolot, R.M., Seda, A., Nawrot, B.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free:
0.133 (Depositor), 0.130 (DCC)
R-Value Work:
0.100 (Depositor), 0.100 (DCC)
R-Value Observed:
0.102 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 28.08 kDa
Atom Count: 2,448
Modeled Residue Count: 231
Deposited Residue Count: 252
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	126	Homo sapiens	Mutation(s): 0 Gene Names: HINT1, HINT, PKCI1, PRKCNH1 EC: 3 (PDB Primary Data), 3.4.22 (UniProt), 3.9.1 (UniProt)
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
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free: 0.133 (Depositor), 0.130 (DCC)
R-Value Work: 0.100 (Depositor), 0.100 (DCC)
R-Value Observed: 0.102 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.031	α = 90
b = 76.364	β = 90
c = 80.864	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-06-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-06-28
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.