2QDM | pdb_00002qdm

Crystal structure of the HePTP catalytic domain C270S/D236A/Q314A mutant

PDB DOI: https://doi.org/10.2210/pdb2QDM/pdb

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

Deposited: 2007-06-21 Released: 2008-06-24
Deposition Author(s): Critton, D.A., Tortajada, A., Page, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.208 (Depositor), 0.206 (DCC)
R-Value Work:
0.164 (Depositor), 0.162 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2QDM

This is version 1.5 of the entry. See complete history.

Literature

Structural basis of substrate recognition by hematopoietic tyrosine phosphatase.

Critton, D.A., Tortajada, A., Stetson, G., Peti, W., Page, R.

To be published.

Macromolecule Content

Total Structure Weight: 35.41 kDa
Atom Count: 2,438
Modeled Residue Count: 286
Deposited Residue Count: 309
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 7	A	309	Homo sapiens	Mutation(s): 3 Gene Names: PTPN7 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P35236 (Homo sapiens) Explore P35236 Go to UniProtKB: P35236
PHAROS: P35236 GTEx: ENSG00000143851
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35236
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 C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.208 (Depositor), 0.206 (DCC)
R-Value Work: 0.164 (Depositor), 0.162 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.324	α = 90
b = 39.041	β = 124.53
c = 83.473	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
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: 2008-06-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-06-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-18
Changes: Refinement description
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2023-01-25
Changes: Database references
Version 1.5: 2023-09-20
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.