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- PDB-3g3e: Crystal structure of human D-amino acid oxidase in complex with h... -

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Basic information

Entry
Database: PDB / ID: 3g3e
TitleCrystal structure of human D-amino acid oxidase in complex with hydroxyquinolin-2(1H)
ComponentsD-amino-acid oxidaseD-amino acid oxidase
KeywordsOXIDOREDUCTASE / d-amino acid oxidase / FAD / Flavoprotein / Peroxisome
Function / homology
Function and homology information


D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / D-serine metabolic process / D-serine catabolic process / proline 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 / D-serine catabolic process / proline 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 / 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
FLAVIN-ADENINE DINUCLEOTIDE / 3-hydroxyquinolin-2(1H)-one / D-amino-acid oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDuplantier, A. / Liu, S.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Discovery, SAR, and pharmacokinetics of a novel 3-Hydroxyquinolin-2(1H)-one series of potent D-amino acid oxidase (DAAO) inhibitors
Authors: Duplantier, A.J. / Becker, S.L. / Bohanon, M.J. / Borzilleri, K.A. / Chrunyk, B.A. / Downs, J.T. / Hu, L.Y. / El-Kattan, A. / James, L.C. / Liu, S. / Lu, J. / Maklad, N. / Mansour, M.N. / ...Authors: Duplantier, A.J. / Becker, S.L. / Bohanon, M.J. / Borzilleri, K.A. / Chrunyk, B.A. / Downs, J.T. / Hu, L.Y. / El-Kattan, A. / James, L.C. / Liu, S. / Lu, J. / Maklad, N. / Mansour, M.N. / Mente, S. / Piotrowski, M.A. / Sakya, S.M. / Sheehan, S. / Steyn, S.J. / Strick, C.A. / Williams, V.A. / Zhang, L.
History
DepositionFeb 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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)163,73712
Polymers159,9504
Non-polymers3,7878
Water5,765320
1
A: D-amino-acid oxidase
B: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8686
Polymers79,9752
Non-polymers1,8934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-38 kcal/mol
Surface area26710 Å2
MethodPISA
2
C: D-amino-acid oxidase
D: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8686
Polymers79,9752
Non-polymers1,8934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-38 kcal/mol
Surface area26700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.063, 82.584, 96.974
Angle α, β, γ (deg.)102.62, 105.43, 110.79
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

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Components

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


Mass: 39987.504 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAO, DAMOX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P14920, D-amino-acid oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-G3E / 3-hydroxyquinolin-2(1H)-one


Mass: 161.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H7NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.07 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 61073 / % possible obs: 88.5 % / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Rmerge(I) obs: 0.068

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Processing

SoftwareName: REFMAC / Version: 5.4.0069 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AN9

1an9


Resolution: 2.2→10 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.899 / SU B: 20.548 / SU ML: 0.259 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.586 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29377 3049 5.1 %RANDOM
Rwork0.23929 ---
obs0.242 56486 88.53 %-
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 mean: 46.903 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20.8 Å2-0.95 Å2
2--3.56 Å20.55 Å2
3----2.39 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10932 0 260 320 11512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02211524
X-RAY DIFFRACTIONr_bond_other_d0.0030.027776
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.97315724
X-RAY DIFFRACTIONr_angle_other_deg1.373318828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78451356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43623.431548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.528151820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7281584
X-RAY DIFFRACTIONr_chiral_restr0.1030.21664
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112820
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022416
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0651.56752
X-RAY DIFFRACTIONr_mcbond_other0.2441.52760
X-RAY DIFFRACTIONr_mcangle_it2.233210920
X-RAY DIFFRACTIONr_scbond_it3.47934772
X-RAY DIFFRACTIONr_scangle_it6.0794.54804
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 4742 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.040.05
Btight positional0.040.05
Ctight positional0.050.05
Dtight positional0.040.05
Atight thermal0.120.5
Btight thermal0.120.5
Ctight thermal0.120.5
Dtight thermal0.120.5
LS refinement shellResolution: 2.2→2.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.481 196 -
Rwork0.432 3681 -
obs--81.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.54380.18460.30220.2268-0.25991.24490.04910.06740.01710.08130.03730.0229-0.1798-0.0023-0.0865-0.0242-0.01240.0217-0.08260.00560.00884.205-38.091828.7971
20.7151-0.08990.16340.3661-0.25421.55090.072-0.1902-0.0256-0.00350.0267-0.0057-0.29860.1172-0.09870.0031-0.03690.0364-0.0722-0.0659-0.024512.3378-43.189271.2188
30.4821-0.0027-0.19180.2429-0.36771.58440.0143-0.1162-0.0211-0.09060.0489-0.00910.2012-0.0063-0.0632-0.04050.0101-0.037-0.05970.0155-0.01294.1455-76.934866.9955
40.8350.0669-0.16060.1662-0.10581.57970.03390.1430.02060.03450.027-0.01350.26480.0868-0.061-0.00320.0102-0.02-0.0917-0.0484-0.017912.4991-71.797324.6021
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 340
2X-RAY DIFFRACTION2B1 - 340
3X-RAY DIFFRACTION3C1 - 340
4X-RAY DIFFRACTION4D1 - 340

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