3N8I | pdb_00003n8i

Crystal structure of the A isoform of human cytoplasmic protein tyrosine phosphatase (HCPTP-A) in complex with 1-naphtylacetic acid

PDB DOI: https://doi.org/10.2210/pdb3N8I/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-05-28 Released: 2011-12-07
Deposition Author(s): Homan, K.T., Balasubramaniam, D., Stauffacher, C.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.203 (Depositor), 0.214 (DCC)
R-Value Work:
0.174 (Depositor), 0.182 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural Characterization of a Secondary Binding Site on Low Molecular Weight Protein Tyrosine Phosphatases

Homan, K.T., Balasubramaniam, D., Stauffacher, C.V.

To be published.

Macromolecule Content

Total Structure Weight: 18.12 kDa
Atom Count: 1,528
Modeled Residue Count: 154
Deposited Residue Count: 157
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low molecular weight phosphotyrosine protein phosphatase	A	157	Homo sapiens	Mutation(s): 0 Gene Names: ACP1, APC1 EC: 3.1.3.48 (PDB Primary Data), 3.1.3.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P24666 (Homo sapiens) Explore P24666 Go to UniProtKB: P24666
PHAROS: P24666 GTEx: ENSG00000143727
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24666
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NLA Query on NLA 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]	NAPHTHALEN-1-YL-ACETIC ACID C₁₂ H₁₀ O₂ PRPINYUDVPFIRX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.203 (Depositor), 0.214 (DCC)
R-Value Work: 0.174 (Depositor), 0.182 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.46	α = 90
b = 56.09	β = 90
c = 95.99	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-12-07

Deposition Author(s):

Balasubramaniam, D.

Stauffacher, C.V.

Revision History (Full details and data files)

Version 1.0: 2011-12-07
Type: Initial release
Version 1.1: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.