RCSB PDB - 6AP9: Crystal Structure of hGSTP1-1 with S-nitrosation of Cys101

 6AP9

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


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), 0.150 (DCC) 
  • R-Value Observed: 0.146 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GDSClick on this verticalbar to view detailsBest fitted GSHClick on this verticalbar to view details

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione S-transferase P
A, B
210Homo sapiensMutation(s): 0 
Gene Names: GSTP1FAEES3GST3
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09211
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDS
Query on GDS

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
OXIDIZED GLUTATHIONE DISULFIDE
C20 H32 N6 O12 S2
YPZRWBKMTBYPTK-BJDJZHNGSA-N
GSH
Query on GSH

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SNC
Query on SNC
A, B
L-PEPTIDE LINKINGC3 H6 N2 O3 SCYS
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), 0.150 (DCC) 
  • R-Value Observed: 0.146 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.148α = 90
b = 90.052β = 98.67
c = 68.872γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GDSClick on this verticalbar to view detailsBest fitted GSHClick on this verticalbar to view details

Entry History 

Deposition Data

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