5VDN | pdb_00005vdn

1.55 Angstrom Resolution Crystal Structure of Glutathione Reductase from Yersinia pestis in Complex with FAD

• PDB DOI: https://doi.org/10.2210/pdb5VDN/pdb

• Classification: HYDROLASE,OXIDOREDUCTASE
• Organism(s): Yersinia pestis KIM10+
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-04-03 Released: 2017-04-19 
• Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Cardona-Correa, A., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.165 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.145 (Depositor) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Model: experimental

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 
• DOI: https://doi.org/10.1128/mra.00200-25
• Primary Citation Related Structures: 
  5TR3, 5TV2, 5TY0, 5U1O, 5U2G, 5U47, 5UE1, 5UME, 5UMG, 5US8, 5USW, 5USX, 5UTX, 5UU6, 5UWY, 5UX9, 5V0I, 5V36, 5VDN, 5VFB, 5VH6, 5VT3, 5WI5, 5WP0, 6AON, 6AOO, 6AWA, 6AZI, 6B4O, 6B5F, 6B8D, 6BAL, 6BK7, 6BLB, 6BQ9, 6BZ0, 6C8Q, 6CMZ, 6CN1, 6CZP, 6E5Y, 6MUQ, 6N0I, 6N7F, 6NBK, 6NFP, 6NKJ, 6PO4, 6PU9, 6PUA, ... Search all related entries


• 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.

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Organizational Affiliation: 
• Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.
Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois, USA.
Biozone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
Biosciences Division, University of California, Riverside, School of Medicine, Riverside, California, USA.
Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 102.98 kDa 
• Atom Count: 8,837 
• Modeled Residue Count: 898 
• Deposited Residue Count: 926 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione oxidoreductase	A, B	463	Yersinia pestis KIM10+	Mutation(s): 0  Gene Names: gor EC: 1.8.1.7
UniProt
Find proteins for Q8CZL0 (Yersinia pestis) Explore Q8CZL0  Go to UniProtKB:  Q8CZL0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
BDF	E [auth A], I [auth B]	beta-D-fructopyranose C6 H12 O6 LKDRXBCSQODPBY-ARQDHWQXSA-N
GOL	F [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	C [auth A], G [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.165 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.145 (Depositor) 
• R-Value Observed: 0.146 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35vdn

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.844	α = 90
b = 125.844	β = 90
c = 124.557	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-19 
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Cardona-Correa, A., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-10-23
  Changes: Structure summary
• Version 1.4: 2026-02-11
  Changes: Database references