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- PDB-3znq: IN VITRO AND IN VIVO INHIBITION OF HUMAN D-AMINO ACID OXIDASE: RE... -

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Basic information

Entry
Database: PDB / ID: 3znq
TitleIN VITRO AND IN VIVO INHIBITION OF HUMAN D-AMINO ACID OXIDASE: REGULATION OF D-SERINE CONCENTRATION IN THE BRAIN
ComponentsD-AMINO-ACID OXIDASED-amino acid oxidase
KeywordsOXIDOREDUCTASE / NEUROTRANSMISSION
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 / Chem-SS8 / D-amino-acid oxidase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsHopkins, S.C. / Heffernan, M.L.R. / Saraswat, L.D. / Bowen, C.A. / Melnick, L. / Hardy, L.W. / Orsini, M.A. / Allen, M.S. / Koch, P. / Spear, K.L. ...Hopkins, S.C. / Heffernan, M.L.R. / Saraswat, L.D. / Bowen, C.A. / Melnick, L. / Hardy, L.W. / Orsini, M.A. / Allen, M.S. / Koch, P. / Spear, K.L. / Foglesong, R.J. / Soukri, M. / Chytil, M. / Fang, Q.K. / Jones, S.W. / Varney, M.A. / Panatier, A. / Oliet, S.H.R. / Pollegioni, L. / Piubelli, L. / Molla, G. / Nardini, M. / Large, T.H.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Structural, Kinetic, and Pharmacodynamic Mechanisms of D-Amino Acid Oxidase Inhibition by Small Molecules.
Authors: Hopkins, S.C. / Heffernan, M.L.R. / Saraswat, L.D. / Bowen, C.A. / Melnick, L. / Hardy, L.W. / Orsini, M.A. / Allen, M.S. / Koch, P. / Spear, K.L. / Foglesong, R.J. / Soukri, M. / Chytil, M. ...Authors: Hopkins, S.C. / Heffernan, M.L.R. / Saraswat, L.D. / Bowen, C.A. / Melnick, L. / Hardy, L.W. / Orsini, M.A. / Allen, M.S. / Koch, P. / Spear, K.L. / Foglesong, R.J. / Soukri, M. / Chytil, M. / Fang, Q.K. / Jones, S.W. / Varney, M.A. / Panatier, A. / Oliet, S.H.R. / Pollegioni, L. / Piubelli, L. / Molla, G. / Nardini, M. / Large, T.H.
History
DepositionFeb 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8665
Polymers79,0422
Non-polymers1,8243
Water93752
1
A: D-AMINO-ACID OXIDASE
hetero molecules

A: D-AMINO-ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1196
Polymers79,0422
Non-polymers2,0784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6200 Å2
ΔGint-35 kcal/mol
Surface area27280 Å2
MethodPISA
2
B: D-AMINO-ACID OXIDASE
hetero molecules

B: D-AMINO-ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6134
Polymers79,0422
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6400 Å2
ΔGint-27.2 kcal/mol
Surface area28290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.471, 84.471, 188.672
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein D-AMINO-ACID OXIDASE / 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) / 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 / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SS8 / 3-PHENETHYL-4H-FURO[3,2-B]PYRROLE-5-CARBOXYLIC ACID


Mass: 253.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.46 Å3/Da / Density % sol: 49.97 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Type: ALS / Wavelength: 0.97
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.75→28.14 Å / Num. obs: 18932 / % possible obs: 90.4 % / Observed criterion σ(I): 1.5 / Redundancy: 3.85 % / Biso Wilson estimate: 71.94 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.5
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 3.85 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.5 / % possible all: 75

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
HKLdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DU8

2du8


Resolution: 2.75→27.65 Å / Cor.coef. Fo:Fc: 0.9322 / Cor.coef. Fo:Fc free: 0.8818 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.391
Details: POOR DENSITY IS PRESENT FOR RESIDUES A25, A26, A27, A28, A297, A302, A335, A336, A337, A338, B25, B26, B27, B28, B29, B30, B56, B57, B58, B59, B99, B100, B101, B174, B175, B194,B195, B196, ...Details: POOR DENSITY IS PRESENT FOR RESIDUES A25, A26, A27, A28, A297, A302, A335, A336, A337, A338, B25, B26, B27, B28, B29, B30, B56, B57, B58, B59, B99, B100, B101, B174, B175, B194,B195, B196, B197, B220, B221, B283, B284, B285, B286, B295, B296, B297,B298, B299, B300, B337, B338. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. FINAL STRUCTURE HAS NO RESIDUES IN THE DISALLOWED REGION OF THE RAMACHANDRAN PLOT AS DEFINED IN THE CCP4 PROCHECK PROGRAM.
RfactorNum. reflection% reflectionSelection details
Rfree0.2552 966 5.11 %RANDOM
Rwork0.1991 ---
obs0.2018 18907 90.13 %-
Displacement parametersBiso mean: 91.44 Å2
Baniso -1Baniso -2Baniso -3
1--6.4458 Å20 Å20 Å2
2---6.4458 Å20 Å2
3---12.8915 Å2
Refine analyzeLuzzati coordinate error obs: 0.559 Å
Refinement stepCycle: LAST / Resolution: 2.75→27.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5438 0 125 52 5615
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085766HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.057871HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1920SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes169HARMONIC2
X-RAY DIFFRACTIONt_gen_planes836HARMONIC5
X-RAY DIFFRACTIONt_it5766HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.28
X-RAY DIFFRACTIONt_other_torsion21.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion720SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6329SEMIHARMONIC4
LS refinement shellResolution: 2.75→2.9 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2701 129 5.55 %
Rwork0.2502 2196 -
all0.2514 2325 -
obs--90.13 %
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)
13.498-1.6633-2.81083.10292.76138.1777-0.0867-0.2501-0.2611-0.2785-0.37250.4117-1.0488-0.36040.4592-0.14420.0637-0.1138-0.2011-0.0505-0.2658-14.75236.501514.6195
23.29192.9125-0.50944.91330.51565.05150.3626-0.53870.3142-0.0661-0.39640.0038-0.67020.11790.03390.1355-0.41440.0593-0.088-0.138-0.38997.309332.509419.3979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1A1 - A357
2X-RAY DIFFRACTION2B1 - B355

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