5BX1

Crystal Structure of PRL-1 complex with compound analogy 3

PDB DOI: https://doi.org/10.2210/pdb5BX1/pdb

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

Deposited: 2015-06-08 Released: 2016-12-21
Deposition Author(s): Liu, S., Bai, Y., Zhang, Z.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.240
R-Value Work: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of PRL-1 complex with compound analogy 3

Liu, S., Bai, Y., Zhang, Z.

To be published.

Macromolecule Content

Total Structure Weight: 18.56 kDa
Atom Count: 1,367
Modelled Residue Count: 153
Deposited Residue Count: 157
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein tyrosine phosphatase type IVA 1	A	157	Homo sapiens	Mutation(s): 0 Gene Names: PTP4A1, PRL1, PTPCAAX1 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q93096 (Homo sapiens) Explore Q93096 Go to UniProtKB: Q93096
PHAROS: Q93096 GTEx: ENSG00000112245
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q93096
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4XA Query on 4XA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	3-(5,6-dimethyl-2H-isoindol-2-yl)-N'-[(E)-furan-2-ylmethylidene]benzohydrazide C₂₂ H₁₉ N₃ O₂ JOUFONRDAYRIBB-FSJBWODESA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.240
R-Value Work: 0.195
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.07	α = 90
b = 76.471	β = 90
c = 86.873	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-12-21

Deposition Author(s):

Liu, S.

Bai, Y.

Zhang, Z.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2016-12-21
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence
Version 1.2: 2022-03-23
Changes: Author supporting evidence, Database references
Version 1.3: 2023-09-27
Changes: Data collection, Refinement description

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5BX1

Crystal Structure of PRL-1 complex with compound analogy 3

Crystal Structure of PRL-1 complex with compound analogy 3

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)