8GYD: Schistosoma japonicum Glutathione S-transferase

Name: PDB 8GYD: Structure of Schistosoma japonicum Glutathione S-transferase bound with the ligand complex of 16
Published: 2023-08-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Structure of Schistosoma japonicum Glutathione S-transferase bound with the ligand complex of 16. Determined by X-ray diffraction at 1.7 Å resolution. Released 23 Aug 2023.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Schistosoma japonicum
Chains: 2
Atoms: 3,935
Mol. weight: 56.77 kDa
Ligands: EOH, 0IH
Released: 23 Aug 2023

Explore 8GYD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8GYD contains 20 α-helices and 12 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	1
α-helix	12-14	3
α-helix	15-23	9
β-strand	29-33	5	1
α-helix	38-44	7
β-strand	57-59	3	1
β-strand	64-66	3	1
α-helix	68-78	11
α-helix	86-110	25
α-helix	115-136	22
β-strand	142	1	2
β-strand	145	1	2
α-helix	150-165	16
α-helix	174-184	11
α-helix	187-193	7

Chain B: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	3
α-helix	12-14	3
α-helix	15-23	9
β-strand	29-33	5	3
α-helix	34	1
α-helix	38-44	7
α-helix	45-47	3
β-strand	57-59	3	3
β-strand	64-66	3	3
α-helix	68-78	11
α-helix	86-109	24
α-helix	115-136	22
β-strand	142	1	4
β-strand	145	1	4
α-helix	150-165	16
α-helix	174-184	11
α-helix	187-193	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutathione S-transferase class-mu 26 kDa isozyme	A, B	protein	232	Schistosoma japonicum	P08515 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8GYD_1 Glutathione S-transferase class-mu 26 kDa isozyme (chains A, B)
HHHHHHLEVLFQGPMSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKF
ELGLEFPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGV
SRIAYSKDFETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMD
PMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPPK

Ligands and cofactors

ID	Name	Formula	Copies
EOH	Ethanol	C2 H6 O	10
0IH	(2R)-2-[[2-(5-chloranylthiophen-2-yl)-4-oxidanylidene-6-[2-(1H-1,2,3,4-tetrazol…	C29 H20 Cl2 N6 O3 S	3

Primary citation

Discovery, SAR Study of GST Inhibitors from a Novel Quinazolin-4(1 H )-one Focused DNA-Encoded Library. Wen, X., Zhang, M., Duan, Z. et al. J Med Chem (2023) 66:11118-11132. DOI 10.1021/acs.jmedchem.2c02129 · PubMed

Other PDB entries of the same protein (UniProt P08515 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8OK1 1.38 Å, WD repeat containing protein 5 (WDR5)- N225A mutant
6JI6 1.5 Å, Crystal structure of glutathione S-transferase complexed and modified with glutathione
6RWD 1.53 Å, Crystal structure of SjGST in complex with GSH and ellagic acid at 1.53 Angstrom…
4WR4 1.6 Å, Crystal Structure of GST Mutated with Halogenated Tyrosine (7bGST-1)
9NME 1.6 Å, SARS-CoV-2 3CLPro in complex with 2-[2-hydroxy-3-(4-isoquinolyl)-4-oxo-6-(trifluoromethyl…
9N4U 1.77 Å, Crystal structure of PAK1 bound to compound R1
1DUG 1.8 Å, Structure of the fibrinogen G chain integrin binding and factor xiiia crosslinking sites…
9NMF 1.8 Å, SARS-CoV-2 3CLPro in complex with 8-(6-amino-3-pyridyl)-2-hydroxy-3-(4-isoquinolyl)-6-(tr…
7AL7 1.8 Å, The Crystal Structure of Human IL-18 in Complex With Human IL-18 Binding Protein
8OKF 1.85 Å, WD repeat containing protein 5 (WDR5)- PER2 peptide
9N48 1.85 Å, Crystal structure of PAK1 bound to compound C1
3CRT 1.9 Å, Structural characterization of an engineered allosteric protein

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