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- PDB-1mar: REFINED 1.8 ANGSTROMS STRUCTURE OF HUMAN ALDOSE REDUCTASE COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1mar
TitleREFINED 1.8 ANGSTROMS STRUCTURE OF HUMAN ALDOSE REDUCTASE COMPLEXED WITH THE POTENT INHIBITOR ZOPOLRESTAT
ComponentsALDOSE REDUCTASE
KeywordsOXIDOREDUCTASE(NADP)
Function / homology
Function and homology information


glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / C21-steroid hormone biosynthetic process / NADP-retinol dehydrogenase / Pregnenolone biosynthesis ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / C21-steroid hormone biosynthetic process / NADP-retinol dehydrogenase / Pregnenolone biosynthesis / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / metanephric collecting duct development / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase (NAD+) activity / aldose reductase (NADPH) activity / epithelial cell maturation / cellular hyperosmotic salinity response / retinoid metabolic process / renal water homeostasis / carbohydrate metabolic process / electron transfer activity / negative regulation of apoptotic process / mitochondrion / extracellular space / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-ZST / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsWilson, D.K. / Quiocho, F.A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Refined 1.8 A structure of human aldose reductase complexed with the potent inhibitor zopolrestat.
Authors: Wilson, D.K. / Tarle, I. / Petrash, J.M. / Quiocho, F.A.
#1: Journal: Science / Year: 1992
Title: An Unlikely Sugar Substrate Site in the 1.65 Angstroms Structure of the Human Aldose Reductase Holoenzyme Implicated in Diabetic Complications
Authors: Wilson, D.K. / Bohren, K.M. / Gabbay, K.H. / Quiocho, F.A.
History
DepositionJul 20, 1993Processing site: BNL
Revision 1.0Jul 20, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALDOSE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9303
Polymers35,7671
Non-polymers1,1632
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.640, 48.040, 40.480
Angle α, β, γ (deg.)64.47, 76.77, 76.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ALDOSE REDUCTASE / Coordinate model: Cα atoms only


Mass: 35767.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P15121, aldose reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-ZST / 3,4-DIHYDRO-4-OXO-3-((5-TRIFLUOROMETHYL-2-BENZOTHIAZOLYL)METHYL)-1-PHTHALAZINE ACETIC ACID


Mass: 419.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H12F3N3O3S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlALR21drop
20.2 mMzopolrestat1drop
33.5 mM2-mercaptoethanol1drop
425 mMcitrate1drop
517 %PEG60001reservoir
67 mM2-mercaptoethanol1reservoir
750 mMcitrate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Num. obs: 26145 / % possible obs: 90.4 % / Num. measured all: 53037 / Rmerge(I) obs: 0.034

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.8→12 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.18 -
obs0.18 25891
Refinement stepCycle: LAST / Resolution: 1.8→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms315 0 77 0 392
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.65
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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