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URL: https://www.rcsb.org/structure/3NP5

⇱ RCSB PDB - 3NP5: Crystal structure of an abridged form of the mature ectodomain of the human receptor-type protein tyrosine phosphatase ICA512/IA-2 AT pH 4.5

251,806
Structures from the PDB archive

1,068,577
Computed Structure Models (CSM)

3NP5 | pdb_00003np5

Crystal structure of an abridged form of the mature ectodomain of the human receptor-type protein tyrosine phosphatase ICA512/IA-2 AT pH 4.5

PDB DOI: https://doi.org/10.2210/pdb3NP5/pdb

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

Deposited: 2010-06-27 Released: 2010-12-29
Deposition Author(s): Primo, M.E., Jakoncic, J., Poskus, E., Ermacora, M.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.239 (Depositor), 0.250 (DCC)
R-Value Work:
0.161 (Depositor), 0.180 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Receptor-Type Protein-Tyrosine Phosphatase Ia-2-Ica512

Primo, M.E., Jakoncic, J., Poskus, E., Ermacora, M.R.

To be published.

Macromolecule Content

Total Structure Weight: 38.63 kDa
Atom Count: 2,874
Modeled Residue Count: 353
Deposited Residue Count: 356
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-type tyrosine-protein phosphatase-like N	A, B, C, D	89	Homo sapiens	Mutation(s): 0 Gene Names: ICA3, ICA512, PTPRN	👁 Image
UniProt & NIH Common Fund Data Resources
Find proteins for Q16849 (Homo sapiens) Explore Q16849 Go to UniProtKB: Q16849
PHAROS: Q16849 GTEx: ENSG00000054356
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q16849
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain E [auth A] MOL2 format, chain F [auth D] MOL2 format, chain E [auth A] mmCIF format, chain F [auth D] mmCIF format, chain E [auth A]	E [auth A], F [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N	👁 Image	Focus chain E [auth A] Focus chain F [auth D] Focus chain E [auth A] Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.239 (Depositor), 0.250 (DCC)
R-Value Work: 0.161 (Depositor), 0.180 (DCC)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.662	α = 90
b = 44.662	β = 90
c = 168.665	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-12-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-12-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-04-18
Changes: Structure summary
Version 1.3: 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.