3BRH | pdb_00003brh

Protein Tyrosine Phosphatase PTPN-22 (Lyp) bound to the mono-Phosphorylated Lck active site peptide

PDB DOI: https://doi.org/10.2210/pdb3BRH/pdb

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

Deposited: 2007-12-21 Released: 2009-02-17
Deposition Author(s): Seidel, R.D., Love, J., Piserchio, A., Cowburn, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.264 (Depositor)
R-Value Work:
0.188 (Depositor)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3BRH

This is version 1.4 of the entry. See complete history.

Literature

Lyp/PTPN22 Phosphatase Domain: Substrate Recognition and Specificity for Src family kinases

Seidel, R., Love, J., Piserchio, A., Cowburn, D.

To be published.

Macromolecule Content

Total Structure Weight: 74.72 kDa
Atom Count: 5,335
Modeled Residue Count: 603
Deposited Residue Count: 634
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 22	A, B	310	Homo sapiens	Mutation(s): 2 Gene Names: PTPN22, PTPN8 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2R2 (Homo sapiens) Explore Q9Y2R2 Go to UniProtKB: Q9Y2R2
PHAROS: Q9Y2R2 GTEx: ENSG00000134242
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y2R2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lck Active Site Peptide	C, D	7	N/A	Mutation(s): 0 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P06239 (Homo sapiens) Explore P06239 Go to UniProtKB: P06239
PHAROS: P06239 GTEx: ENSG00000182866
Entity Groups
UniProt Group	P06239
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.264 (Depositor)
R-Value Work: 0.188 (Depositor)
R-Value Observed: 0.191 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.85	α = 90
b = 48.51	β = 103.49
c = 119.97	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
SHARP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-02-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-02-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations, Source and taxonomy, Structure summary
Version 1.4: 2024-02-21
Changes: Data collection

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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.