6AP9 | pdb_00006ap9

Crystal Structure of hGSTP1-1 with S-nitrosation of Cys101

PDB DOI: https://doi.org/10.2210/pdb6AP9/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-08-17 Released: 2018-08-22
Deposition Author(s): Kumari, V., Ji, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.181 (Depositor), 0.180 (DCC)
R-Value Work:
0.146 (Depositor), 0.146 (DCC)
R-Value Observed:
0.146 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Cysteine S-nitrosylation of hGSTP1-1 by nitric oxide (NO)-releasing prodrugs

Kumari, V., Dyba, M.A., Ji, X.

To be published.

Macromolecule Content

Total Structure Weight: 49.36 kDa
Atom Count: 4,359
Modeled Residue Count: 421
Deposited Residue Count: 422
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase P	A, B	210	Homo sapiens	Mutation(s): 0 Gene Names: GSTP1, FAEES3, GST3 EC: 2.5.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for P09211 (Homo sapiens) Explore P09211 Go to UniProtKB: P09211
PHAROS: P09211 GTEx: ENSG00000084207
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09211
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDS Query on GDS Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], J [auth B]	OXIDIZED GLUTATHIONE DISULFIDE C₂₀ H₃₂ N₆ O₁₂ S₂ YPZRWBKMTBYPTK-BJDJZHNGSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
GSH Query on GSH Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	F [auth A], L [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], M [auth B], N [auth B], O [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNC Query on SNC	A, B	L-PEPTIDE LINKING	C₃ H₆ N₂ O₃ S		CYS

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.181 (Depositor), 0.180 (DCC)
R-Value Work: 0.146 (Depositor), 0.146 (DCC)
R-Value Observed: 0.146 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.148	α = 90
b = 90.052	β = 98.67
c = 68.872	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-08-22

Deposition Author(s):

Kumari, V.

Ji, X.

Revision History (Full details and data files)

Version 1.0: 2018-08-22
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description