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- PDB-5zja: human D-amino acid oxidase complexed with 5-chlorothiophene-2-car... -

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Basic information

Entry
Database: PDB / ID: 5zja
Titlehuman D-amino acid oxidase complexed with 5-chlorothiophene-2-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-2-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.
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 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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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
Water1,910106
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 area6260 Å2
ΔGint-37 kcal/mol
Surface area26250 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 area6270 Å2
ΔGint-38 kcal/mol
Surface area26280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.294, 182.641, 51.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 38699.910 Da / Num. of mol.: 4 / Fragment: UNP residues 1-340
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 / Comment: FAD*YM
#3: Chemical
ChemComp-9E9 / 5-chloro thiophene-2-carboxylic acid / 5-chloranylthiophene-2-carboxylic acid


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


Mass: 18.015 Da / Num. of mol.: 106 / 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: 45.65 %
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, and 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→49.23 Å / Num. obs: 44404 / % possible obs: 100 % / Redundancy: 8.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.108 / Net I/σ(I): 9.7
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 1.786 / Num. unique obs: 4593 / CC1/2: 0.517 / Rpim(I) all: 0.983

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2du8

2du8


Resolution: 2.6→49.229 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.64
RfactorNum. reflection% reflection
Rfree0.2598 2089 4.72 %
Rwork0.2009 --
obs0.2038 44280 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→49.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11180 0 0 106 11286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411508
X-RAY DIFFRACTIONf_angle_d0.88415700
X-RAY DIFFRACTIONf_dihedral_angle_d14.4116820
X-RAY DIFFRACTIONf_chiral_restr0.0851672
X-RAY DIFFRACTIONf_plane_restr0.0032008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.66050.38241270.32692760X-RAY DIFFRACTION100
2.6605-2.7270.36461240.30942772X-RAY DIFFRACTION100
2.727-2.80070.35481320.28752777X-RAY DIFFRACTION100
2.8007-2.88320.33721300.2842800X-RAY DIFFRACTION100
2.8832-2.97620.35571380.27092774X-RAY DIFFRACTION100
2.9762-3.08260.34581280.26652758X-RAY DIFFRACTION100
3.0826-3.2060.29011210.25132831X-RAY DIFFRACTION100
3.206-3.35180.32641440.23222765X-RAY DIFFRACTION100
3.3518-3.52850.27731360.20332794X-RAY DIFFRACTION100
3.5285-3.74950.24381670.19212772X-RAY DIFFRACTION100
3.7495-4.03890.25141410.17232832X-RAY DIFFRACTION100
4.0389-4.44510.19731530.15362802X-RAY DIFFRACTION100
4.4451-5.08770.21561410.15192873X-RAY DIFFRACTION100
5.0877-6.40780.2171570.17872871X-RAY DIFFRACTION100
6.4078-49.23780.23091500.16643010X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 123.8747 Å / Origin y: 50.0923 Å / Origin z: 38.4576 Å
111213212223313233
T0.1654 Å20.0026 Å20.0024 Å2-0.1964 Å2-0.0054 Å2--0.1979 Å2
L0.0725 °2-0.0386 °20.0344 °2-0.291 °2-0.0137 °2--0.4777 °2
S0.0049 Å °-0.0037 Å °0.0172 Å °-0.0385 Å °-0.0265 Å °-0.0113 Å °0.0676 Å °0.0368 Å °-0 Å °
Refinement TLS groupSelection details: all

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