5KMC | pdb_00005kmc

Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) non-nucleotidic covalent intermediate complex

PDB DOI: https://doi.org/10.2210/pdb5KMC/pdb

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

Deposited: 2016-06-26 Released: 2017-06-28
Deposition Author(s): Maize, K.M., Finzel, B.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.174 (Depositor), 0.176 (DCC)
R-Value Work:
0.159 (Depositor), 0.160 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural Biology for Drug Design: Applications in Two Systems

(2016) Thesis

Macromolecule Content

Total Structure Weight: 28.43 kDa
Atom Count: 2,069
Modeled Residue Count: 227
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine triad nucleotide-binding protein 1	A, B	129	Homo sapiens	Mutation(s): 0 Gene Names: HINT1, HINT 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49773
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6UU Query on 6UU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	[2-(1~{H}-indol-3-yl)ethylamino]phosphonic acid C₁₀ H₁₃ N₂ O₃ P LZBMOXGGHSGOHA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.174 (Depositor), 0.176 (DCC)
R-Value Work: 0.159 (Depositor), 0.160 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.093	α = 90
b = 46.151	β = 94.66
c = 63.994	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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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: 2017-07-26
Changes: Database references
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.