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), 0.180 (DCC)
R-Value Work:
0.156 (Depositor), 0.160 (DCC)
R-Value Observed:
0.158 (Depositor)

wwPDB Validation 3D Report Full Report

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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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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), 0.180 (DCC)
R-Value Work: 0.156 (Depositor), 0.160 (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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Ligand Structure Quality Assessment

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

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.