6DLG

Crystal structure of a SHIP1 surface entropy reduction mutant

PDB DOI: https://doi.org/10.2210/pdb6DLG/pdb

Classification: HYDROLASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-06-01 Released: 2019-06-05
Deposition Author(s): Gardill, B.R., Cheung, S.T., Mui, A.L., Van Petegem, F.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.200
R-Value Work: 0.178
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

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

Literature

Interleukin-10 and Small Molecule SHIP1 Allosteric Regulators Trigger Anti-Inflammatory Effects Through SHIP1/STAT3 Complexes

Chamberlain, T.C., Cheung, S.T., Yoon, J.S.J., Ming-Lum, A., Gardill, B.R., Shakibakho, S., Dzananovic, E., Ban, F., Samiea, A., Jawanda, K., Priatel, J., Krystal, G., Ong, C.J., Cherkasov, A., Andersen, R.J., McKenna, S.A., Van Petegem, F., Mui, A.L.

(2020) Biorxiv

DOI: https://doi.org/10.1101/2020.05.29.123943

Macromolecule Content

Total Structure Weight: 52.57 kDa
Atom Count: 3,878
Modelled Residue Count: 421
Deposited Residue Count: 463
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1	A	463	Mus musculus	Mutation(s): 3 Gene Names: Inpp5d, 7a33, Ship, Ship1 EC: 3.1.3.86
UniProt
Find proteins for Q9ES52 (Mus musculus) Explore Q9ES52 Go to UniProtKB: Q9ES52
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9ES52
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-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: 0.200
R-Value Work: 0.178
R-Value Observed: 0.179
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.098	α = 90
b = 73.2	β = 90
c = 124.207	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-06-05

Deposition Author(s):

Van Petegem, F.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP-84539

Revision History (Full details and data files)

Version 1.0: 2019-06-05
Type: Initial release
Version 1.1: 2020-01-08
Changes: Author supporting evidence
Version 1.2: 2020-06-17
Changes: Database references
Version 1.3: 2024-03-13
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.