Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37866.25 
• Atom Count: 7890 
• Residue Count: 321 
• Unique protein chains: 1

5QDI

PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000157a

• DOI: 10.2210/pdb5QDI/pdb
• Deposition Group: G_1002043 (changed state)

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 2 


• Deposited: 2018-08-30 Released: 2018-10-10 
• Deposition Author(s): Keedy, D.A., Hill, Z.B., Biel, J.T., Kang, E., Rettenmaier, T.J., Brandao-Neto, J., von Delft, F., Wells, J.A., Fraser, J.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.623 Å
• R-Value Free: 0.218 
• R-Value Work: 0.188 

Literature

An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.

Keedy, D.A., Hill, Z.B., Biel, J.T., Kang, E., Rettenmaier, T.J., Brandao-Neto, J., Pearce, N.M., von Delft, F., Wells, J.A., Fraser, J.S.

(2018) Elife 7: --

• PubMed: 29877794 
• DOI: 10.7554/eLife.36307
• Primary Citation of Related Structures:  
  6BAI, 6B95, 6B90, 6B8Z, 6B8X, 6B8T, 6B8E, 5QGF, 5QGE, 5QGD, 5QGC, 5QGB, 5QGA, 5QG9, 5QG8, 5QG7, 5QG6, 5QG5, 5QG4, 5QG3, 5QG2, 5QG1, 5QG0, 5QFZ, 5QFY, 5QFX, 5QFW, 5QFV, 5QFU, 5QFT, 5QFS, 5QFR, 5QFQ, 5QFP, 5QFO, 5QFN, 5QFM, 5QFL, 5QFJ, 5QFK,
  6BAI, 6B95, 6B90, 6B8Z, 6B8X, 6B8T, 6B8E, 5QGF, 5QGE, 5QGD, 5QGC, 5QGB, 5QGA, 5QG9, 5QG8, 5QG7, 5QG6, 5QG5, 5QG4, 5QG3, 5QG2, 5QG1, 5QG0, 5QFZ, 5QFY, 5QFX, 5QFW, 5QFV, 5QFU, 5QFT, 5QFS, 5QFR, 5QFQ, 5QFP, 5QFO, 5QFN, 5QFM, 5QFL, 5QFJ, 5QFK, 5QFI, 5QFH, 5QFG, 5QFF, 5QFE, 5QFD, 5QFC, 5QFB, 5QFA, 5QF9, 5QF8, 5QF7, 5QF6, 5QF5, 5QF4, 5QF3, 5QF2, 5QF1, 5QF0, 5QEZ, 5QEY, 5QEX, 5QEW, 5QEV, 5QEU, 5QET, 5QES, 5QER, 5QEQ, 5QEP, 5QEO, 5QEN, 5QEM, 5QEL, 5QEK, 5QEJ, 5QEI, 5QEH, 5QEG, 5QEF, 5QEE, 5QED, 5QEC, 5QEB, 5QEA, 5QE9, 5QE8, 5QE7, 5QE6, 5QE5, 5QE4, 5QE3, 5QE2, 5QE1, 5QE0, 5QDZ, 5QDY, 5QDX, 5QDW, 5QDV, 5QDU, 5QDT, 5QDS, 5QDR, 5QDQ, 5QDP, 5QDO, 5QDN, 5QDM, 5QDL, 5QDK, 5QDJ, 5QDH, 5QDG, 5QDF, 5QDE


• PubMed Abstract: 
  

Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here, we have identified allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal 'hidden' low-occupancy conformational states for protein and ligands. Our results converge on allosteric sites that are conformationally coupled to the active-site WPD loop and are hotspots for fragment binding. Targeting one of these sites with covalently tethered molecules or mutations allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure, revealed here by multitemperature crystallography, can elucidate allosteric mechanisms and open new doors for long-range control of protein function.

---

Organizational Affiliation: 

Crystal and Structural Chemistry Group, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands.,Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.,Diamond Light Source, Didcot, United Kingdom.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.,Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Tyrosine-protein phosphatase non-receptor type 1	A	321	Homo sapiens	Mutation(s): 2  Gene Names: PTPN1 (PTP1B) EC: 3.1.3.48
Find proteins for P18031 (Homo sapiens) Go to Gene View: PTPN1 Go to UniProtKB:  P18031

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
JFM	A	N-(2-phenylethyl)methanesulfonamide C9 H13 N O2 S JGDDFCYMSLNOGJ-UHFFFAOYSA-N
TRS	A	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL TRIS BUFFER C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.623 Å
• R-Value Free: 0.218 
• R-Value Work: 0.188 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 89.877	α = 90.00
b = 89.877	β = 90.00
c = 106.634	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-08-30 
• Released Date: 2018-10-10 
• Deposition Author(s): Keedy, D.A., Hill, Z.B., Biel, J.T., Kang, E., Rettenmaier, T.J., Brandao-Neto, J., von Delft, F., Wells, J.A., Fraser, J.S.

Revision History 

• Version 1.0: 2018-10-10
  Type: Initial release
• Version 1.1: 2019-02-06
  Type: Data collection, Database references, Structure summary