6N7F | pdb_00006n7f

1.90 Angstrom Resolution Crystal Structure of Glutathione Reductase from Streptococcus pyogenes in Complex with FAD.

PDB DOI: https://doi.org/10.2210/pdb6N7F/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptococcus pyogenes serotype M1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-11-27 Released: 2018-12-12
Deposition Author(s): Minasov, G., Shuvalova, L., Shabalin, I.G., Grabowski, M., Olphie, A., Cardona-Correa, A., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.210 (Depositor), 0.210 (DCC)
R-Value Work:
0.169 (Depositor), 0.180 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.

Inniss, N.L., Minasov, G., Chang, C., Tan, K., Kim, Y., Maltseva, N., Stogios, P., Filippova, E., Michalska, K., Osipiuk, J., Jaroszewki, L., Godzik, A., Savchenko, A., Joachimiak, A., Anderson, W.F., Satchell, K.J.F.

(2025) Microbiol Resour Announc 14: e0020025-e0020025

PubMed: 40391899 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/mra.00200-25
Primary Citation of Related Structures:
5TR3, 5TV2, 5TY0, 5U1O, 5U2G, 5U47, 5UE1, 5UME, 5US8, 5USW, 5USX, 5UTX, 5UU6, 5UWY, 5UX9, 5V36, 5VDN, 5VFB, 5VH6, 5WI5, 5WP0, 6AON, 6AOO, 6AWA, 6AZI, 6B4O, 6B5F, 6B8D, 6BAL, 6BK7, 6BLB, 6BQ9, 6BZ0, 6C8Q, 6CMZ, 6CN1, 6CZP, 6E5Y, 6MUQ, 6N0I, 6N7F, 6NFP, 6NKJ, 6PO4, 6PU9, 6PUA, 6PXA, 6W2Z, 9BZN, 9BZQ

PubMed Abstract:
Antibiotic resistance remains a leading cause of severe infections worldwide. Small changes in protein sequence can impact antibiotic efficacy. Here, we report deposition of 58 X-ray crystal structures of bacterial proteins that are known targets for antibiotics, which expands knowledge of structural variation to support future antibiotic discovery or modifications.

Organizational Affiliation

Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.

Macromolecule Content

Total Structure Weight: 202.07 kDa
Atom Count: 16,456
Modeled Residue Count: 1,802
Deposited Residue Count: 1,812
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glutathione reductase (GR)	A, B, C, D	453	Streptococcus pyogenes serotype M1	Mutation(s): 0 Gene Names: gor, SPy_0813 EC: 1.8.1.7
UniProt
Find proteins for Q9A0E2 (Streptococcus pyogenes serotype M1) Explore Q9A0E2 Go to UniProtKB: Q9A0E2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9A0E2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain Z [auth D] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Z [auth D]	E [auth A], M [auth B], S [auth C], Z [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain Z [auth D]
RBF Query on RBF Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	RIBOFLAVIN C₁₇ H₂₀ N₄ O₆ AUNGANRZJHBGPY-SCRDCRAPSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain T [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C]	AA [auth D], G [auth A], N [auth B], T [auth C]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain G [auth A] Focus chain N [auth B] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain G [auth A] Focus chain N [auth B] Focus chain T [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain FA [auth D] MOL2 format, chain FA [auth D] mmCIF format, chain FA [auth D]	FA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Interactions & Density Focus chain FA [auth D]
BCT Query on BCT Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Q [auth B] SDF format, chain K [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain K [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain K [auth A]	BA [auth D] CA [auth D] DA [auth D] EA [auth D] I [auth A] BA [auth D], CA [auth D], DA [auth D], EA [auth D], I [auth A], J [auth A], K [auth A], L [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.210 (Depositor), 0.210 (DCC)
R-Value Work: 0.169 (Depositor), 0.180 (DCC)
R-Value Observed: 0.171 (Depositor)

Diffraction Data: https://doi.org/10.18430/m36n7f

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.4	α = 67.13
b = 86.65	β = 74.15
c = 86.67	γ = 74.11

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-12-12

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2018-12-12
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.2: 2026-02-11
Changes: Database references, Structure summary