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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.269 (Depositor), 0.268 (DCC)
R-Value Work:
0.217 (Depositor), 0.217 (DCC)
R-Value Observed:
0.224 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/prot.20642
Primary Citation Related Structures:
1YZ4

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 36.52 kDa
Atom Count: 2,617
Modeled Residue Count: 315
Deposited Residue Count: 320
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H1R2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BOG Query on BOG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [auth B], G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.269 (Depositor), 0.268 (DCC)
R-Value Work: 0.217 (Depositor), 0.217 (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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-11-01

Deposition Author(s):

Revision History (Full details and data files)

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