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- PDB-3w4k: Crystal Structure of human DAAO in complex with coumpound 13 -

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Basic information

Entry
Database: PDB / ID: 3w4k
TitleCrystal Structure of human DAAO in complex with coumpound 13
ComponentsD-amino-acid oxidase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / D-serine metabolic process / proline catabolic process / D-amino acid catabolic process / D-serine catabolic process / Glyoxylate metabolism and glycine degradation / dopamine biosynthetic process / neutrophil-mediated killing of gram-negative bacterium ...D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / D-serine metabolic process / proline catabolic process / D-amino acid catabolic process / D-serine catabolic process / Glyoxylate metabolism and glycine degradation / dopamine biosynthetic process / neutrophil-mediated killing of gram-negative bacterium / presynaptic active zone / peroxisomal matrix / digestion / FAD binding / cell projection / Peroxisomal protein import / extracellular region / identical protein binding / cytosol / cytoplasm
Similarity search - Function
D-amino acid oxidase, conserved site / D-amino-acid oxidase / D-amino acid oxidases signature. / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich ...D-amino acid oxidase, conserved site / D-amino-acid oxidase / D-amino acid oxidases signature. / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-hydroxy-6-(2-phenylethyl)pyridazin-4(1H)-one / FLAVIN-ADENINE DINUCLEOTIDE / D-amino-acid oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.86 Å
AuthorsHondo, T. / Warizaya, M. / Niimi, T. / Namatame, I. / Yamaguchi, T. / Nakanishi, K. / Hamajima, T. / Harada, K. / Sakashita, H. / Matsumoto, Y. ...Hondo, T. / Warizaya, M. / Niimi, T. / Namatame, I. / Yamaguchi, T. / Nakanishi, K. / Hamajima, T. / Harada, K. / Sakashita, H. / Matsumoto, Y. / Orita, M. / Watanabe, T. / Takeuchi, M.
CitationJournal: J.Med.Chem. / Year: 2013
Title: 4-Hydroxypyridazin-3(2H)-one Derivatives as Novel d-Amino Acid Oxidase Inhibitors.
Authors: Hondo, T. / Warizaya, M. / Niimi, T. / Namatame, I. / Yamaguchi, T. / Nakanishi, K. / Hamajima, T. / Harada, K. / Sakashita, H. / Matsumoto, Y. / Orita, M. / Takeuchi, M.
History
DepositionJan 9, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _software.version
Revision 1.2Mar 20, 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

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Assembly

Deposited unit
A: D-amino-acid oxidase
B: D-amino-acid oxidase
C: D-amino-acid oxidase
D: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,09112
Polymers158,0844
Non-polymers4,0078
Water00
1
A: D-amino-acid oxidase
B: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0456
Polymers79,0422
Non-polymers2,0044
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-42 kcal/mol
Surface area26470 Å2
MethodPISA
2
C: D-amino-acid oxidase
D: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0456
Polymers79,0422
Non-polymers2,0044
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-35 kcal/mol
Surface area26880 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14720 Å2
ΔGint-93 kcal/mol
Surface area50760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.663, 182.463, 50.844
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
D-amino-acid oxidase / DAAO / DAMOX / DAO


Mass: 39520.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAO, DAMOX / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14920, D-amino-acid oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-3LD / 3-hydroxy-6-(2-phenylethyl)pyridazin-4(1H)-one


Mass: 216.236 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H12N2O2

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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: 2.2 Å3/Da / Density % sol: 43.98 % / Mosaicity: 0.8 °
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 8
Details: 10-15% (w/v) PEG 4000, 0.1M sodium citrate pH8.0, 0.2M ammonium dihydrogen phosphate, 10% (v/v) glycerol, sitting drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Apr 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.86→48.12 Å / Num. obs: 31226 / % possible obs: 94.1 % / Redundancy: 3.63 % / Rmerge(I) obs: 0.179 / Χ2: 3.57 / Net I/σ(I): 4.3 / Scaling rejects: 4220
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
2.86-2.963.550.5191.61129131073.5325495.5
2.96-3.083.590.4351.91137930983.4724395.5
3.08-3.223.650.4182.11169931133.8934094.9
3.22-3.393.610.3282.61160831314.2229495.1
3.39-3.63.580.2633.31140230654.6643894.1
3.6-3.883.420.214.11096830804.5642993.5
3.88-4.273.450.1664.91110731004.3641793.5
4.27-4.893.730.12661199030963.3143494
4.89-6.163.930.116.71304931982.449594.6
6.16-48.123.80.0738.81317532381.8787691.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK7.1SSIdata scaling
d*TREK7.1SSIdata reduction
AMoREphasing
REFMAC5.5.0066refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→38.95 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.842 / WRfactor Rfree: 0.2699 / WRfactor Rwork: 0.1972 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7436 / SU B: 0.004 / SU ML: 0 / SU R Cruickshank DPI: 0.3359 / SU Rfree: 0.4626 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.431 / ESU R Free: 0.635 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3441 1566 5.1 %RANDOM
Rwork0.2334 ---
obs0.2392 30809 92.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 99.61 Å2 / Biso mean: 46.4544 Å2 / Biso min: 10.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.86→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10932 0 276 0 11208
LS refinement shellResolution: 2.86→2.934 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 108 -
Rwork0.374 2114 -
all-2222 -
obs--93.32 %

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