7SO8 | pdb_00007so8

Crystal structure of Glutathione S-Transferase from Shrimp Litopenaeus vannamei in complex with silver ions and a molecules of Glutathione binding in G-site and H-site

PDB DOI: https://doi.org/10.2210/pdb7SO8/pdb

Classification: TRANSFERASE
Organism(s): Penaeus vannamei
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-10-29 Released: 2022-11-02
Deposition Author(s): Escudero-Garcia, A., Rudino-Pinera, E., Miranda-Blancas, R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.260 (Depositor), 0.260 (DCC)
R-Value Work:
0.191 (Depositor), 0.190 (DCC)
R-Value Observed:
0.195 (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

Inhibition of GST class Mu of the shrimp Litopenaeus vannamei by binding silver ions in H-site.

Escudero-Garcia, A., Rudino-Pinera, E.

To be published.

Macromolecule Content

Total Structure Weight: 208.05 kDa
Atom Count: 15,875
Modeled Residue Count: 1,752
Deposited Residue Count: 1,752
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione transferase	A B [auth C] C [auth E] D [auth G] E [auth H] A, B [auth C], C [auth E], D [auth G], E [auth H], F, G [auth B], H [auth D]	219	Penaeus vannamei	Mutation(s): 0 EC: 2.5.1.18
UniProt
Find proteins for Q49SB0 (Penaeus vannamei) Explore Q49SB0 Go to UniProtKB: Q49SB0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q49SB0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH (Subject of Investigation/LOI) Query on GSH Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth C] SDF format, chain M [auth E] SDF format, chain O [auth G] SDF format, chain R [auth F] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain V [auth D] SDF format, chain Q [auth F] SDF format, chain P [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth C] MOL2 format, chain M [auth E] MOL2 format, chain O [auth G] MOL2 format, chain R [auth F] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth F] MOL2 format, chain P [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth C] mmCIF format, chain M [auth E] mmCIF format, chain O [auth G] mmCIF format, chain R [auth F] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth F] mmCIF format, chain P [auth H]	I [auth A] J [auth C] M [auth E] O [auth G] P [auth H] I [auth A], J [auth C], M [auth E], O [auth G], P [auth H], Q [auth F], R [auth F], S [auth B], T [auth B], V [auth D]	GLUTATHIONE C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain I [auth A] Focus chain J [auth C] Focus chain M [auth E] Focus chain O [auth G] Focus chain P [auth H] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth C] Focus chain M [auth E] Focus chain O [auth G] Focus chain P [auth H] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth D]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C] mmCIF format, chain K [auth C]	K [auth C]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]
AG (Subject of Investigation/LOI) Query on AG Download Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain N [auth G] SDF format, chain L [auth E] MOL2 format, chain U [auth D] MOL2 format, chain N [auth G] MOL2 format, chain L [auth E] mmCIF format, chain U [auth D] mmCIF format, chain N [auth G] mmCIF format, chain L [auth E]	L [auth E], N [auth G], U [auth D]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N		Interactions Focus chain L [auth E] Focus chain N [auth G] Focus chain U [auth D] Interactions & Density Focus chain L [auth E] Focus chain N [auth G] Focus chain U [auth D]