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- PDB-7u9u: Crystal structure of human D-amino acid oxidase in complex with i... -

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Basic information

Entry
Database: PDB / ID: 7u9u
TitleCrystal structure of human D-amino acid oxidase in complex with inhibitor
ComponentsD-amino-acid oxidase
KeywordsOXIDOREDUCTASE/INHIBITOR / FAD / Flavoprotein / Oxidoreductase / Peroxisome / 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
Similarity search - Domain/homology
BENZOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / Chem-M89 / D-amino-acid oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsSkene, R.J. / Bell, J.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery of a Novel Class of d-Amino Acid Oxidase Inhibitors Using the Schrodinger Computational Platform.
Authors: Tang, H. / Jensen, K. / Houang, E. / McRobb, F.M. / Bhat, S. / Svensson, M. / Bochevarov, A. / Day, T. / Dahlgren, M.K. / Bell, J.A. / Frye, L. / Skene, R.J. / Lewis, J.H. / Osborne, J.D. / ...Authors: Tang, H. / Jensen, K. / Houang, E. / McRobb, F.M. / Bhat, S. / Svensson, M. / Bochevarov, A. / Day, T. / Dahlgren, M.K. / Bell, J.A. / Frye, L. / Skene, R.J. / Lewis, J.H. / Osborne, J.D. / Tierney, J.P. / Gordon, J.A. / Palomero, M.A. / Gallati, C. / Chapman, R.S.L. / Jones, D.R. / Hirst, K.L. / Sephton, M. / Chauhan, A. / Sharpe, A. / Tardia, P. / Dechaux, E.A. / Taylor, A. / Waddell, R.D. / Valentine, A. / Janssens, H.B. / Aziz, O. / Bloomfield, D.E. / Ladha, S. / Fraser, I.J. / Ellard, J.M.
History
DepositionMar 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,0226
Polymers79,0422
Non-polymers1,9814
Water3,855214
1
A: D-amino-acid oxidase
hetero molecules

A: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8576
Polymers79,0422
Non-polymers1,8154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6980 Å2
ΔGint-22 kcal/mol
Surface area27050 Å2
MethodPISA
2
B: D-amino-acid oxidase
hetero molecules

B: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1886
Polymers79,0422
Non-polymers2,1464
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6220 Å2
ΔGint-39 kcal/mol
Surface area26280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.806, 73.403, 79.799
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.: 2
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.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-M89 / (3R)-3-(5,6-dioxo-1,4,5,6-tetrahydropyrazin-2-yl)-2,3-dihydro-1,4-benzoxathiine-7-carbonitrile


Mass: 287.294 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C13H9N3O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.28 Å3/Da / Density % sol: 45.94 % / Mosaicity: 0.15 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1M Succinate pH 7.0, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9765 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.66→49.45 Å / Num. obs: 85786 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 14.3 / Num. measured all: 559017 / Scaling rejects: 3
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 6.6 % / Rmerge(I) obs: 2.074 / Num. unique obs: 4218 / CC1/2: 0.315 / Rpim(I) all: 0.868 / Rrim(I) all: 2.253 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
PRIME-Xrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DU8

2du8


Resolution: 1.66→40.56 Å / Rfactor Rfree error: 0.01 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4361 5.1 %RANDOM
Rwork0.202 ---
obs-85711 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Bsol: 52.35 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso max: 111.76 Å2 / Biso mean: 39.3 Å2 / Biso min: 17.13 Å2
Refinement stepCycle: LAST / Resolution: 1.66→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5460 0 135 214 5809
Refine LS restraintsType: OPLS 2005X
LS refinement shellResolution: 1.66→1.72 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.402 436 5.1 %
Rwork0.386 8571 -
obs--100 %

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