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- PDB-6szp: High resolution crystal structure of human DDAH-1 in complex with... -

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Basic information

Entry
Database: PDB / ID: 6szp
TitleHigh resolution crystal structure of human DDAH-1 in complex with N-(4-Aminobutyl)-N'-(2-Methoxyethyl)guanidine
ComponentsN(G),N(G)-dimethylarginine dimethylaminohydrolase 1
KeywordsHYDROLASE / dimethylarginine dimethylaminohydrolase / guanidine inhibitor / induced fit / prodrug
Function / homology
Function and homology information


dimethylargininase / dimethylargininase activity / citrulline metabolic process / negative regulation of cellular response to hypoxia / arginine metabolic process / regulation of systemic arterial blood pressure / negative regulation of vascular permeability / nitric oxide metabolic process / amino acid binding / catalytic activity ...dimethylargininase / dimethylargininase activity / citrulline metabolic process / negative regulation of cellular response to hypoxia / arginine metabolic process / regulation of systemic arterial blood pressure / negative regulation of vascular permeability / nitric oxide metabolic process / amino acid binding / catalytic activity / nitric oxide mediated signal transduction / arginine catabolic process / eNOS activation / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / negative regulation of cell population proliferation / extracellular exosome / metal ion binding / cytosol
Similarity search - Function
Dimethylarginine dimethylaminohydrolase / N,N dimethylarginine dimethylhydrolase, eukaryotic / Arginine deiminase / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta
Similarity search - Domain/homology
Chem-M3B / N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsHennig, S. / Vetter, I.R. / Schade, D.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery ofN-(4-Aminobutyl)-N'-(2-methoxyethyl)guanidine as the First Selective, Nonamino Acid, Catalytic Site Inhibitor of Human Dimethylarginine Dimethylaminohydrolase-1 (hDDAH-1).
Authors: Lunk, I. / Litty, F.A. / Hennig, S. / Vetter, I.R. / Kotthaus, J. / Altmann, K.S. / Ott, G. / Havemeyer, A. / Carillo Garcia, C. / Clement, B. / Schade, D.
History
DepositionOct 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9434
Polymers32,5681
Non-polymers3743
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Activity assay performed
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-2 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.945, 54.945, 87.684
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 / Dimethylarginine dimethylaminohydrolase 1 / DDAHI / Dimethylargininase-1


Mass: 32568.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDAH1, DDAH / Plasmid: pQE30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pREP4 / References: UniProt: O94760, dimethylargininase
#2: Chemical ChemComp-M3B / (1~{S})-~{N}'-(4-azanylbutyl)-~{N}"-(2-methoxyethyl)methanetriamine


Mass: 190.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H22N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: reservoir: 0.1M MES pH 6.0 + 30% PEG6000 drop: 1+1 (v/v) cryo protectant: reservoir + 20%(v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.008 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.76→46.56 Å / Num. obs: 25915 / % possible obs: 99.6 % / Redundancy: 6.67 % / CC1/2: 0.998 / Net I/σ(I): 11.98
Reflection shellResolution: 1.76→1.8 Å / Mean I/σ(I) obs: 1.52 / Num. unique obs: 1824 / CC1/2: 0.675 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→46.56 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 24.95
RfactorNum. reflection% reflection
Rfree0.2303 1296 5 %
Rwork0.2006 --
obs0.2022 25915 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.37 Å2 / Biso mean: 36.0639 Å2 / Biso min: 17.49 Å2
Refinement stepCycle: final / Resolution: 1.76→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 47 137 2294
Biso mean--44.95 41.14 -
Num. residues----275
LS refinement shellResolution: 1.76→1.8 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3707 138 -
Rwork0.3101 2625 -
obs--96 %

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