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- PDB-5zj9: human D-amino acid oxidase complexed with 5-chlorothiophene-3-car... -

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Basic information

Entry
Database: PDB / ID: 5zj9
Titlehuman D-amino acid oxidase complexed with 5-chlorothiophene-3-carboxylic acid
ComponentsD-amino-acid oxidase
KeywordsOXIDOREDUCTASE / D-amino acid / flavoenzyme
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-serine catabolic process / D-amino acid catabolic process / Glyoxylate metabolism and glycine degradation / dopamine biosynthetic process / presynaptic active zone ...D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / D-serine metabolic process / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / Glyoxylate metabolism and glycine degradation / dopamine biosynthetic process / presynaptic active zone / neutrophil-mediated killing of gram-negative bacterium / peroxisomal matrix / digestion / FAD binding / Peroxisomal protein import / identical protein binding / cytoplasm / cytosol
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
5-chloro thiophene-3-carboxylic acid / FLAVIN-ADENINE DINUCLEOTIDE / D-amino-acid oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKato, Y. / Hin, N. / Maita, N. / Thomas, A.G. / Kurosawa, S. / Rojas, C. / Yorita, K. / Slusher, B.S. / Fukui, K. / Tsukamoto, T.
Funding support Japan, United States, 2items
OrganizationGrant numberCountry
a grant for Enzyme Research from the Japan Foundation for Applied Enzymology Japan
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01MH091387 United States
CitationJournal: Eur J Med Chem / Year: 2018
Title: Structural basis for potent inhibition of d-amino acid oxidase by thiophene carboxylic acids
Authors: Kato, Y. / Hin, N. / Maita, N. / Thomas, A.G. / Kurosawa, S. / Rojas, C. / Yorita, K. / Slusher, B.S. / Fukui, K. / Tsukamoto, T.
History
DepositionMar 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Structure summary
Category: database_2 / entity / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_audit_support.funding_organization
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)158,59212
Polymers154,8004
Non-polymers3,7938
Water4,053225
1
A: D-amino-acid oxidase
B: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2966
Polymers77,4002
Non-polymers1,8964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-38 kcal/mol
Surface area26800 Å2
MethodPISA
2
C: D-amino-acid oxidase
D: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2966
Polymers77,4002
Non-polymers1,8964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-39 kcal/mol
Surface area26530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.140, 182.730, 51.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-553-

HOH

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Components

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


Mass: 38699.910 Da / Num. of mol.: 4 / Fragment: UNP residues 1-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAO, DAMOX / Production host: Escherichia coli (E. coli) / 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-9E6 / 5-chloro thiophene-3-carboxylic acid / 5-chloranylthiophene-3-carboxylic acid


Mass: 162.594 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H3ClO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15%(w/v) PEG 4000, 0.2M ammonium acetate, 0.1M Na citrate at pH 8.0, 10%(v/v) glycerol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→39.15 Å / Num. obs: 44351 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.126 / Net I/σ(I): 9.5
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 1.348 / Num. unique obs: 4577 / CC1/2: 0.731 / Rpim(I) all: 0.741

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Processing

Software
NameVersionClassification
PHENIX1.12refinement
MOSFLMdata reduction
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2du8

2du8


Resolution: 2.6→39.15 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.255 --
Rwork0.2188 --
obs0.2206 44351 100 %
Refinement stepCycle: LAST / Resolution: 2.6→39.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10932 0 248 225 11405

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