3VUR | pdb_00003vur

Crystal structure of Bombyx mori sigma-class glutathione transferase in complex with glutathionesulfonic acid

PDB DOI: https://doi.org/10.2210/pdb3VUR/pdb

Classification: TRANSFERASE
Organism(s): Bombyx mori
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-07-05 Released: 2013-07-10
Deposition Author(s): Yamamoto, K., Higashiura, A., Nakagawa, A., Suzuki, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.36 Å
R-Value Free:
0.182 (Depositor), 0.184 (DCC)
R-Value Work:
0.156 (Depositor), 0.158 (DCC)
R-Value Observed:
0.158 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of Bombyx mori sigma-class glutathione transferase in complex with glutathionesulfonic acid

Yamamoto, K., Higashiura, A., Nakagawa, A., Suzuki, M.

To be published.

Macromolecule Content

Total Structure Weight: 23.96 kDa
Atom Count: 1,960
Modeled Residue Count: 203
Deposited Residue Count: 204
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase sigma	A	204	Bombyx mori	Mutation(s): 0 Gene Names: GST sigma EC: 2.5.1.18
UniProt
Find proteins for Q5CCJ4 (Bombyx mori) Explore Q5CCJ4 Go to UniProtKB: Q5CCJ4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5CCJ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTS Query on GTS 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]	GLUTATHIONE SULFONIC ACID C₁₀ H₁₇ N₃ O₉ S QGWRMTHFAZVWAM-WDSKDSINSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.36 Å
R-Value Free: 0.182 (Depositor), 0.184 (DCC)
R-Value Work: 0.156 (Depositor), 0.158 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.41	α = 90
b = 57.41	β = 90
c = 209.665	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-07-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-07-10
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.