7XC0 | pdb_00007xc0

Crystal structure of Human RPTPH

• PDB DOI: https://doi.org/10.2210/pdb7XC0/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-03-22 Released: 2022-07-06 
• Deposition Author(s): Kim, M., Ryu, S.E.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.207 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the catalytic domain of human RPTPH.

Kim, M., Ryu, S.E.

(2022) Acta Crystallogr F Struct Biol Commun 78: 265-269

• PubMed: 35787553 
• DOI: https://doi.org/10.1107/S2053230X22006173
• Primary Citation Related Structures: 
  7XC0


• PubMed Abstract: 
  

  Receptor-type protein tyrosine phosphatases (RPTPs) receive extracellular stimuli and transfer them into cells. They regulate cell growth, differentiation and death via specific signals. They have also been implicated in cancer, diabetes and neurological diseases. RPTPH, a member of the type 3 RPTP (R3-PTP) family, is an important regulator of colorectal cancer and hepatic carcinoma. Despite its importance in drug development, the structure of RPTPH has not yet been resolved. Here, the crystal structure of the catalytic domain of RPTPH was determined at 1.56 Å resolution. Despite similarities to other R3-PTPs in its overall structure, RPTPH exhibited differences in its loop regions and side-chain conformations. Compared with other R3-PTPs, RPTPH has unique side chains near its active site that may confer specificity for inhibitor binding. Therefore, detailed information on the structure of RPTPH provides clues for the development of specific inhibitors.

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Organizational Affiliation: 
• Department of Bioengineering, College of Engineering, Hanyang University, Seoul 04673, Republic of Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.32 kDa 
• Atom Count: 2,512 
• Modeled Residue Count: 287 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-type tyrosine-protein phosphatase H	A	291	Homo sapiens	Mutation(s): 2  Gene Names: PTPRH, SAP1 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HD43 (Homo sapiens) Explore Q9HD43  Go to UniProtKB:  Q9HD43
PHAROS:  Q9HD43 GTEx:  ENSG00000080031

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.207 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M37XC0

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.46	α = 90
b = 56.46	β = 90
c = 80.447	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-07-06 
Deposition Author(s): Kim, M., Ryu, S.E.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2022-07-06
  Type: Initial release
  
• Version 1.1: 2022-07-20
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description