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- PDB-2h5l: S-Adenosylhomocysteine hydrolase containing NAD and 3-deaza-D-eri... -

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Basic information

Entry
Database: PDB / ID: 2h5l
TitleS-Adenosylhomocysteine hydrolase containing NAD and 3-deaza-D-eritadenine
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / S-Adenosylhomocysteine / Inhibitor / Hypocholesterolemic activity
Function / homology
Function and homology information


adenosylselenohomocysteinase activity / S-adenosylhomocysteine catabolic process / Sulfur amino acid metabolism / circadian sleep/wake cycle / adenyl nucleotide binding / chronic inflammatory response to antigenic stimulus / adenosylhomocysteinase / adenosylhomocysteinase activity / Methylation / S-adenosylmethionine cycle ...adenosylselenohomocysteinase activity / S-adenosylhomocysteine catabolic process / Sulfur amino acid metabolism / circadian sleep/wake cycle / adenyl nucleotide binding / chronic inflammatory response to antigenic stimulus / adenosylhomocysteinase / adenosylhomocysteinase activity / Methylation / S-adenosylmethionine cycle / response to nutrient / NAD binding / melanosome / one-carbon metabolic process / response to hypoxia / copper ion binding / endoplasmic reticulum / identical protein binding / nucleus / cytosol
Similarity search - Function
Adenosylhomocysteinase-like / Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain ...Adenosylhomocysteinase-like / Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3DD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYamada, T. / Komoto, J. / Takusagawa, F.
CitationJournal: Biochem.Pharm. / Year: 2007
Title: Structure and function of eritadenine and its 3-deaza analogues: Potent inhibitors of S-adenosylhomocysteine hydrolase and hypocholesterolemic agents.
Authors: Yamada, T. / Komoto, J. / Lou, K. / Ueki, A. / Hua, D.H. / Sugiyama, K. / Takata, Y. / Ogawa, H. / Takusagawa, F.
History
DepositionMay 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Adenosylhomocysteinase
B: Adenosylhomocysteinase
C: Adenosylhomocysteinase
D: Adenosylhomocysteinase
E: Adenosylhomocysteinase
F: Adenosylhomocysteinase
G: Adenosylhomocysteinase
H: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)387,05124
Polymers379,7268
Non-polymers7,32516
Water5,224290
1
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
C: Adenosylhomocysteinase
D: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,52512
Polymers189,8634
Non-polymers3,6638
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28050 Å2
ΔGint-130 kcal/mol
Surface area50550 Å2
MethodPISA
2
E: Adenosylhomocysteinase
F: Adenosylhomocysteinase
G: Adenosylhomocysteinase
H: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,52512
Polymers189,8634
Non-polymers3,6638
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28180 Å2
ΔGint-130 kcal/mol
Surface area50420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.50, 178.60, 112.66
Angle α, β, γ (deg.)90, 107.9, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase


Mass: 47465.711 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ahcy / Production host: Escherichia coli (E. coli) / References: UniProt: P10760, adenosylhomocysteinase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-3DD / (2R,3R)-4-(4-AMINO-1H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-2,3-DIHYDROXYBUTANOIC ACID


Mass: 252.227 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H12N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5
Details: 15% PGE-8000, 50 mM MES, 2% glycerol, pH 6.5, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 78969 / Num. obs: 78969 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.9 Å / % possible all: 80.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLORmodel building
X-PLOR98refinement
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2833 7650 RANDOM
Rwork0.248 --
all0.2488 76545 -
obs0.2488 76545 -
Refine analyzeLuzzati coordinate error obs: 0.034 Å
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26552 0 496 290 27338
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.12
X-RAY DIFFRACTIONx_dihedral_angle_d25.8

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