1F2E | pdb_00001f2e

STRUCTURE OF SPHINGOMONAD, GLUTATHIONE S-TRANSFERASE COMPLEXED WITH GLUTATHIONE

PDB DOI: https://doi.org/10.2210/pdb1F2E/pdb

Classification: TRANSFERASE
Organism(s): Sphingomonas paucimobilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2000-05-24 Released: 2000-06-21
Deposition Author(s): Nishio, T., Watanabe, T., Patel, A., Wang, Y., Lau, P.C.K., Grochulski, P., Li, Y., Cygler, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.236 (Depositor), 0.236 (DCC)
R-Value Work:
0.198 (Depositor), 0.199 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Properties of a Sphingomonad and Marine Bacterium Beta-Class Glutathione S-Transferases and Crystal Structure of the Former Complex with Glutathione

Nishio, T., Watanabe, T., Patel, A., Wang, Y., Lau, P.C.K., Grochulski, P., Li, Y., Cygler, M.

To be published.

Macromolecule Content

Total Structure Weight: 85.57 kDa
Atom Count: 6,424
Modeled Residue Count: 804
Deposited Residue Count: 804
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTATHIONE S-TRANSFERASE	A, B, C, D	201	Sphingomonas paucimobilis	Mutation(s): 0 EC: 2.5.1.18
UniProt
Find proteins for O33705 (Sphingomonas paucimobilis) Explore O33705 Go to UniProtKB: O33705
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O33705
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH) Query on PRD_002593	E [auth A], F [auth B], G [auth C], H [auth D]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.236 (Depositor), 0.236 (DCC)
R-Value Work: 0.198 (Depositor), 0.199 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.505	α = 90
b = 44.792	β = 98.6
c = 116.459	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2000-06-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-06-21
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2011-12-21
Changes: Non-polymer description
Version 1.4: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary