8WFY | pdb_00008wfy

The Crystal Structure of SHP2 from Biortus.

PDB DOI: https://doi.org/10.2210/pdb8WFY/pdb

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

Deposited: 2023-09-20 Released: 2023-11-22
Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Qi, J., Li, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.317 (Depositor), 0.319 (DCC)
R-Value Work:
0.237 (Depositor), 0.240 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

The Crystal Structure of SHP2 from Biortus.

Wang, F., Cheng, W., Yuan, Z., Qi, J., Li, J.

To be published.

Macromolecule Content

Total Structure Weight: 121.07 kDa
Atom Count: 8,400
Modeled Residue Count: 980
Deposited Residue Count: 1,050
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 11	A, B	525	Homo sapiens	Mutation(s): 0 Gene Names: PTPN11 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q06124 (Homo sapiens) Explore Q06124 Go to UniProtKB: Q06124
PHAROS: Q06124 GTEx: ENSG00000179295
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06124
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5OD (Subject of Investigation/LOI) Query on 5OD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine C₁₆ H₁₉ Cl₂ N₅ YGUFCDOEKKVKJK-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.317 (Depositor), 0.319 (DCC)
R-Value Work: 0.237 (Depositor), 0.240 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.617	α = 90
b = 213.636	β = 96.846
c = 55.707	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-11-22
Type: Initial release

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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.