[English] 日本語
Yorodumi
- PDB-3grs: REFINED STRUCTURE OF GLUTATHIONE REDUCTASE AT 1.54 ANGSTROMS RESO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3grs
TitleREFINED STRUCTURE OF GLUTATHIONE REDUCTASE AT 1.54 ANGSTROMS RESOLUTION
ComponentsGLUTATHIONE REDUCTASE
KeywordsOXIDOREDUCTASE (FLAVOENZYME)
Function / homology
Function and homology information


glutathione-disulfide reductase / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / glutathione-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / NADP binding ...glutathione-disulfide reductase / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / glutathione-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / NADP binding / flavin adenine dinucleotide binding / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / external side of plasma membrane / mitochondrion / extracellular exosome / cytosol
Similarity search - Function
Glutathione reductase, eukaryote/bacterial / Pyridine nucleotide-disulphide oxidoreductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily ...Glutathione reductase, eukaryote/bacterial / Pyridine nucleotide-disulphide oxidoreductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / Glutathione reductase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.54 Å
AuthorsSchulz, G.E. / Karplus, P.A.
Citation
Journal: J.Mol.Biol. / Year: 1987
Title: Refined structure of glutathione reductase at 1.54 A resolution.
Authors: Karplus, P.A. / Schulz, G.E.
#1: Journal: Eur.J.Biochem. / Year: 1988
Title: Inhibition of Human Glutathione Reductase by the Nitrosourea Drugs 1,3-Bis(2-Chloroethyl)-1-Nitrosurea and 1-(2-Chloroethyl)-3-(2-Hydroxyethyl)-1-Nitrosourea
Authors: Karplus, P.A. / Krauth-Siegel, R.L. / Schirmer, R.H. / Schulz, G.E.
#2: Journal: Eur.J.Biochem. / Year: 1984
Title: Interaction of a Glutathione S-Conjugate with Glutathione Reductase. Kinetic and X-Ray Crystallographic Studies
Authors: Bilzer, M. / Krauth-Siegel, R.L. / Schirmer, R.H. / Akerboom, T.P.M. / Sies, H. / Schulz, G.E.
#3: Journal: J.Mol.Biol. / Year: 1983
Title: Comparison of the Three-Dimensional Protein and Nucleotide Structure of the Fad-Binding Domain of P-Hydroxybenzoate Hydroxylase with the Fad-as Well as Nadph-Binding Domains of Glutathione Reductase
Authors: Wierenga, R.K. / Drenth, J. / Schulz, G.E.
#4: Journal: J.Biol.Chem. / Year: 1983
Title: The Catalytic Mechanism of Glutathione Reductase as Derived from X-Ray Diffraction Analyses of Reaction Intermediates
Authors: Pai, E.F. / Schulz, G.E.
#5: Journal: J.Mol.Biol. / Year: 1982
Title: Fad-Binding Site of Glutathione Reductase
Authors: Schulz, G.E. / Schirmer, R.H. / Pai, E.F.
#6: Journal: Eur.J.Biochem. / Year: 1982
Title: Glutathione Reductase from Human Erythrocytes. The Sequences of the Nadph Domain and of the Interface Domain
Authors: Krauth-Siegel, R.L. / Blatterspiel, R. / Saleh, M. / Schiltz, E. / Schirmer, R.H. / Untucht-Grau, R.
#7: Journal: J.Mol.Biol. / Year: 1981
Title: Three-Dimensional Structure of Glutathione Reductase at 2 Angstroms Resolution
Authors: Thieme, R. / Pai, E.F. / Schirmer, R.H. / Schulz, G.E.
#8: Journal: J.Mol.Biol. / Year: 1980
Title: Gene Duplication in Glutathione Reductase
Authors: Schulz, G.E.
#9: Journal: FEBS Lett. / Year: 1979
Title: The C-Terminal Fragment of Human Glutathione Reductase Contains the Postulated Catalytic Histidine
Authors: Untucht-Grau, R. / Schulz, G.E. / Schirmer, R.H.
#10: Journal: Nature / Year: 1978
Title: The Structure of the Flavoenzyme Glutathione Reductase
Authors: Schulz, G.E. / Schirmer, R.H. / Sachsenheimer, W. / Pai, E.F.
#11: Journal: J.Mol.Biol. / Year: 1977
Title: Low Resolution Structure of Human Erythrocyte Glutathione Reductase
Authors: Zappe, H.A. / Krohne-Ehrich, G. / Schulz, G.E.
#12: Journal: FEBS Lett. / Year: 1975
Title: Crystals of Human Erythrocyte Glutathione Reductase
Authors: Schulz, G.E. / Zappe, H. / Worthington, D.J. / Rosemeyer, M.A.
History
DepositionFeb 5, 1988Processing site: BNL
SupersessionApr 16, 1988ID: 2GRS
Revision 1.0Apr 16, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUTATHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5173
Polymers51,6361
Non-polymers8812
Water9,422523
1
A: GLUTATHIONE REDUCTASE
hetero molecules

A: GLUTATHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,0346
Polymers103,2722
Non-polymers1,7614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area10060 Å2
ΔGint-80 kcal/mol
Surface area37080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.800, 84.500, 63.200
Angle α, β, γ (deg.)90.00, 90.00, 58.70
Int Tables number5
Space group name H-MB112
Atom site foot note1: RESIDUES PRO 375 AND PRO 468 ARE CIS-PROLINES.
2: CYS 90 FORMS A DISULFIDE BRIDGE WITH ITS COUNTERPART IN THE OTHER SUBUNIT. (SEE REMARK 4 ABOVE FOR THE TRANSFORMATION TO GENERATE THIS SECOND SUBUNIT.)
3: DISCRETE DISORDER WAS OBSERVED FOR RESIDUES 20, 99, 119, 190, 202, 231, 276, 292, 373, 406, 420 AND 457.

-
Components

#1: Protein GLUTATHIONE REDUCTASE


Mass: 51636.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00390, EC: 1.6.4.2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.2 Mammonium sulfate1reservoir
20.1 Mpotassium phosphate1reservoir

-
Data collection

Reflection
*PLUS
Highest resolution: 1.54 Å / Lowest resolution: 9999 Å / Num. obs: 78959 / Rmerge F obs: 0.059

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.54→10 Å / Rfactor Rwork: 0.186
Details: THIS ENTRY PRESENTS THE OXIDIZED FORM (E). DISCRETE DISORDER WAS OBSERVED FOR RESIDUES 20, 99, 119, 190, 202, 231, 276, 292, 373, 406, 420 AND 457.
Refinement stepCycle: LAST / Resolution: 1.54→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3499 0 58 523 4080
Refinement
*PLUS
Num. reflection obs: 77690 / Highest resolution: 1.54 Å / Lowest resolution: 10 Å / Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.025
X-RAY DIFFRACTIONo_angle_deg2.4

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more