5BX1 | pdb_00005bx1

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.240 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.201 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of PRL-1 complex with compound analogy 3

Liu, S., Bai, Y., Zhang, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4XA	B [auth A]	3-(5,6-dimethyl-2H-isoindol-2-yl)-N'-[(E)-furan-2-ylmethylidene]benzohydrazide C22 H19 N3 O2 JOUFONRDAYRIBB-FSJBWODESA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.240 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.201 (DCC) 

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

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Liu, S., Bai, Y., Zhang, Z.

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

Revision History  

• 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
• Version 1.4: 2024-11-06
  Changes: Structure summary