3PGT

CRYSTAL STRUCTURE OF HGSTP1-1[I104] COMPLEXED WITH THE GSH CONJUGATE OF (+)-ANTI-BPDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.159 
  • R-Value Observed: 0.156 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Structure and function of residue 104 and water molecules in the xenobiotic substrate-binding site in human glutathione S-transferase P1-1.

Ji, X.Blaszczyk, J.Xiao, B.O'Donnell, R.Hu, X.Herzog, C.Singh, S.V.Zimniak, P.

(1999) Biochemistry 38: 10231-10238

  • DOI: https://doi.org/10.1021/bi990668u
  • Primary Citation of Related Structures:  
    3PGT, 4PGT

  • PubMed Abstract: 

    Two variants of human class pi glutathione (GSH) S-transferase 1-1 with either isoleucine or valine in position 104 (hGSTP1-1[I104] and hGSTP1-1[V104]) have distinct activity toward (+)-anti-7, 8-dihydroxy-9,10-oxy-7,8,9,10-tetrahydrobenzo[a]pyrene [(+)-anti-BPDE]. To elucidate their structure-function relationship, we determined the crystal structures of the two variants in complex with GSBpd, the GSH conjugate of (+)-anti-BPDE, at 2.1 and 2.0 A resolution, respectively. The crystal structures reveal that residue 104 in the xenobiotic substrate-binding site (H-site) dictates the binding modes of the product molecule GSBpd with the following three consequences. First, the distance between the hydroxyl group of Y7 and the sulfur atom of GSBpd is 5.9 A in the hGSTP1-1[I104].GSBpd complex versus 3.2 A in the V104 variant. Second, one of the hydroxyl groups of GSBpd forms a direct hydrogen bond with R13 in hGSTP1-1[V104].GSBpd; in contrast, this hydrogen bond is not observed in the I104 complex. Third, in the hydrophilic portion of the H-site of the I104 complex, five H-site water molecules [Ji, X., et al. (1997) Biochemistry 36, 9690-9702] are observed, whereas in the V104 complex, two of the five have been displaced by the Bpd moiety of GSBpd. Although there is no direct hydrogen bond between Y108 (OH) and the hydroxyl groups of GSBpd, indirect hydrogen bonds mediated by water molecules are observed in both complexes, supporting the previously suggested role of the hydroxyl group of Y108 as an electrophilic participant in the addition of GSH to epoxides.


  • Organizational Affiliation

    ABL-Basic Research Program, National Cancer Institute-Frederick Cancer Research and Development Center, Maryland 21702, USA. jix@ncifcrf.gov


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (GLUTATHIONE S-TRANSFERASE)
A, B
210Homo sapiensMutation(s): 0 
Gene Names: GTP_HUMAN
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GBX
Query on GBX

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B]
2-AMINO-4-[1-(CARBOXYMETHYL-CARBAMOYL)-2-(9-HYDROXY-7,8-DIOXO-7,8,9,10-TETRAHYDRO-BENZO[DEF]CHRYSEN-10-YLSULFANYL)-ETHYLCARBAMOYL]-BUTYRIC ACID
C30 H27 N3 O9 S
DUWOHLGCRJLRRU-HVYZTVOGSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
N [auth B],
O [auth B]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
J [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
J [auth B],
K [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.159 
  • R-Value Observed: 0.156 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.83α = 90
b = 89.71β = 97.76
c = 68.41γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
SHELXLrefinement
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-09-01
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Data collection
  • Version 1.4: 2019-11-13
    Changes: Database references
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.6: 2023-09-06
    Changes: Refinement description