3UBL | pdb_00003ubl

Crystal structure of glutathione transferase (TARGET EFI-501770) from leptospira interrogans with gsh bound

PDB DOI: https://doi.org/10.2210/pdb3UBL/pdb

Classification: TRANSFERASE
Organism(s): Leptospira interrogans serovar Lai str. 56601
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-10-24 Released: 2011-11-09
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Zencheck, W.D., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Imker, H.J., Armstrong, R.N., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.235 (Depositor), 0.237 (DCC)
R-Value Work:
0.200 (Depositor), 0.202 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Glutathione S-Transferase from Leptospira Interrogans

Patskovsky, Y., Toro, R., Bhosle, R., Zencheck, W.D., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Imker, H.J., Armstrong, R.N., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 56.89 kDa
Atom Count: 3,634
Modeled Residue Count: 419
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione transferase	A, B	242	Leptospira interrogans serovar Lai str. 56601	Mutation(s): 0 Gene Names: gst, LA_2623
UniProt
Find proteins for Q8F2Y8 (Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)) Explore Q8F2Y8 Go to UniProtKB: Q8F2Y8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8F2Y8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain L [auth B]	C [auth A], L [auth B]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A], M [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	G [auth A], I [auth A], J [auth A], N [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B]	H [auth A], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain O [auth B]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain P [auth B] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B]	K [auth A], P [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain K [auth A] Focus chain P [auth B] Interactions & Density Focus chain K [auth A] Focus chain P [auth B]

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	C [auth A], L [auth B]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.235 (Depositor), 0.237 (DCC)
R-Value Work: 0.200 (Depositor), 0.202 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.591	α = 90
b = 82.591	β = 90
c = 175.701	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-11-09

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2011-11-09
Type: Initial release
Version 1.1: 2011-12-21
Changes: Non-polymer description
Version 1.2: 2012-02-29
Changes: Database references, Structure summary
Version 1.3: 2018-01-24
Changes: Structure summary
Version 1.4: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description