3D9C | pdb_00003d9c

Crystal Structure PTP1B complex with aryl Seleninic acid

PDB DOI: https://doi.org/10.2210/pdb3D9C/pdb

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

Deposited: 2008-05-27 Released: 2008-09-23
Deposition Author(s): Abdo, M., Liu, S., Zhou, B., Walls, C.D., Knapp, S., Zhang, Z.-Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.274 (Depositor)
R-Value Work:
0.218 (Depositor), 0.222 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Seleninate in place of phosphate: irreversible inhibition of protein tyrosine phosphatases.

Abdo, M., Liu, S., Zhou, B., Walls, C.D., Wu, L., Knapp, S., Zhang, Z.Y.

(2008) J Am Chem Soc 130: 13196-13197

PubMed: 18781746 Search on PubMed
DOI: https://doi.org/10.1021/ja804489m
Primary Citation Related Structures:
3D9C

PubMed Abstract:
A homotyrosine based seleninic acid irreversibly inhibits protein tyrosine phosphatases by forming a covalent selenosulfide linkage with the active site cysteine sulfhydryl specifically. The details of the event are revealed by model synthetic studies and by kinetic, mass spectrometric, and crystallographic characterization.

Organizational Affiliation

Department of Chemistry and Chemical Biology, Rutgers The State University of New Jersey, Piscataway, New Jersey 08854, USA.

Macromolecule Content

Total Structure Weight: 37.77 kDa
Atom Count: 2,369
Modeled Residue Count: 282
Deposited Residue Count: 321
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 1	A	321	Homo sapiens	Mutation(s): 0 Gene Names: PTPN1, PTP1B EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens) Explore P18031 Go to UniProtKB: P18031
PHAROS: P18031 GTEx: ENSG00000196396
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18031
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZYZ Query on ZYZ Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(4-{(2S)-2-[(tert-butoxycarbonyl)amino]-3-methoxy-3-oxopropyl}phenyl)methaneseleninic acid C₁₆ H₂₃ N O₆ Se CEUSGDKNGCAEAX-ZDUSSCGKSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.274 (Depositor)
R-Value Work: 0.218 (Depositor), 0.222 (DCC)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.279	α = 90
b = 89.279	β = 90
c = 105.656	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-09-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-09-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations