Macromolecule Content

Total Structure Weight: 53.38 kDa
Atom Count: 4672
Modelled Residue Count: 460
Deposited Residue Count: 463
Unique protein chains: 1

6XY7

Human SHIP1 with magnesium and phosphate bound to the active site

DOI: 10.2210/pdb6XY7/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2020-01-29 Released: 2020-02-26
Deposition Author(s): Bradshaw, W.J., Scacioc, A., Fernandez-Cid, A., Mckinley, G., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Gileadi, O.
Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.09 Å
R-Value Free: 0.159
R-Value Work: 0.136

wwPDB Validation 3D Report Full Report

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

Literature

Human SHIP1 with magnesium and phosphate bound to the active site

Bradshaw, W.J., Scacioc, A., Fernandez-Cid, A., Mckinley, G., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Gileadi, O.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1	AAA	463	Homo sapiens	Mutation(s): 0 Gene Names: INPP5D, SHIP, SHIP1 EC: 3.1.3.86 (PDB Primary Data), 3.1.3.56 (PDB Primary Data), 3.1.3.36 (PDB Primary Data)
Find proteins for Q92835 (Homo sapiens) Explore Q92835 Go to UniProtKB: Q92835
NIH Common Fund Data Resources
PHAROS: Q92835 GTEx: ENSG00000168918
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain G [AAA] MOL2 format, chain G [AAA]	AAA	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Ligand Interaction
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [AAA] MOL2 format, chain C [AAA]	AAA	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Ligand Interaction
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain D [AAA] SDF format, chain E [AAA] SDF format, chain F [AAA] MOL2 format, chain D [AAA] MOL2 format, chain E [AAA] MOL2 format, chain F [AAA]	AAA	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [AAA] MOL2 format, chain B [AAA]	AAA	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.09 Å
R-Value Free: 0.159
R-Value Work: 0.136
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.5	α = 90
b = 79.088	β = 90
c = 89.255	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2020-01-29
Released Date: 2020-02-26

Deposition Author(s):

Fernandez-Cid, A.

Burgess-Brown, N.A.

Arrowsmith, C.H.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	1U54AG065187-01

Revision History (Full details and data files)

Version 1.0: 2020-02-26
Type: Initial release
Version 1.1: 2020-11-11
Changes: Source and taxonomy

RCSB PDB is 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.