1YZ4 | pdb_00001yz4

Crystal structure of DUSP15

• PDB DOI: https://doi.org/10.2210/pdb1YZ4/pdb

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


• Deposited: 2005-02-28 Released: 2005-11-01 
• Deposition Author(s): Kim, S.J., Ryu, S.E., Jeong, D.G., Yoon, T.S., Kim, J.H., Cho, Y.H., Jeong, S.K., Lee, J.W., Son, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.269 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Literature

Crystal structure of the catalytic domain of human VHY, a dual-specificity protein phosphatase

Yoon, T.S., Jeong, D.G., Kim, J.H., Cho, Y.H., Son, J.H., Lee, J.W., Ryu, S.E., Kim, S.J.

(2005) Proteins 61: 694-697

• PubMed: 16170801 
• DOI: https://doi.org/10.1002/prot.20642
• Primary Citation of Related Structures:  
  1YZ4

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Organizational Affiliation: 

Systemic Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.

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: 36.52 kDa 
• Atom Count: 2,617 
• Modelled Residue Count: 315 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dual specificity phosphatase-like 15 isoform a	A, B	160	Homo sapiens	Mutation(s): 1  EC: 3.1.3.48 (PDB Primary Data), 3.1.3.16 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1R2 (Homo sapiens) Explore Q9H1R2  Go to UniProtKB:  Q9H1R2
GTEx:  ENSG00000149599

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG	C [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
SO4	D [auth A], E [auth B], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.269 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.233	α = 90
b = 76.395	β = 90
c = 101.429	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
EPMR	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-01 
Deposition Author(s): Kim, S.J., Ryu, S.E., Jeong, D.G., Yoon, T.S., Kim, J.H., Cho, Y.H., Jeong, S.K., Lee, J.W., Son, J.H.

Revision History  

• Version 1.0: 2005-11-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2021-11-10
  Changes: Database references, Structure summary
• Version 1.5: 2024-05-29
  Changes: Data collection