2QCT | pdb_00002qct

Structure of Lyp with inhibitor I-C11

• PDB DOI: https://doi.org/10.2210/pdb2QCT/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-06-19 Released: 2007-11-20 
• Deposition Author(s): Yu, X., Sun, J.P., Zhang, Z.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Lyp and its complex with a selective inhibitor

Yu, X., Sun, J.P., He, Y.T., Zhou, B., Liu, S.J., Zhang, Z.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 74.1 kDa 
• Atom Count: 4,666 
• Modeled Residue Count: 567 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 22	A, B	313	Homo sapiens	Mutation(s): 0  Gene Names: PTPN22, PTPN8 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2R2 (Homo sapiens) Explore Q9Y2R2  Go to UniProtKB:  Q9Y2R2
PHAROS:  Q9Y2R2 GTEx:  ENSG00000134242

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
561	C [auth A]	6-HYDROXY-3-{(4R)-1-[4-(1-NAPHTHYLAMINO)-4-OXOBUTYL]-1,2,3-TRIAZOLIDIN-4-YL}-1-BENZOFURAN-5-CARBOXYLIC ACID C25 H24 N4 O5 KWXBSQWOCREJEL-NRFANRHFSA-N
EDO	D [auth A], E [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.904	α = 90
b = 147.945	β = 98.04
c = 46.157	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-20 
Deposition Author(s): Yu, X., Sun, J.P., Zhang, Z.Y.

Revision History  

• Version 1.0: 2007-11-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description