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

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Basic information

Entry
Database: PDB / ID: 3znn
TitleIN VITRO AND IN VIVO INHIBITION OF HUMAN D-AMINO ACID OXIDASE: REGULATION OF D-SERINE CONCENTRATION IN THE BRAIN
ComponentsD-AMINO-ACID OXIDASE
KeywordsOXIDOREDUCTASE / FLAVOOXIDASE / NEUROTRANSMISSION
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 / 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
4H-THIENO[3,2-B]PYROLE-5-CARBOXYLIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / D-amino-acid oxidase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.2Dec 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)81,96017
Polymers79,0422
Non-polymers2,91915
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-34.3 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.830, 78.680, 99.960
Angle α, β, γ (deg.)90.00, 92.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein D-AMINO-ACID OXIDASE / DAAO / DAMOX / DAO / D-AMINO ACID OXIDASE


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


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


Mass: 167.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5NO2S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.23 Å3/Da / Density % sol: 44.78 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU SATURN / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→19.46 Å / Num. obs: 51647 / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Redundancy: 1.73 % / Biso Wilson estimate: 34.85 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 7.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.67 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 1.8 / % possible all: 93.9

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
d*TREKdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DU8

2du8


Resolution: 1.9→15.54 Å / Cor.coef. Fo:Fc: 0.9554 / Cor.coef. Fo:Fc free: 0.9279 / SU R Cruickshank DPI: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.195 / SU Rfree Blow DPI: 0.176 / SU Rfree Cruickshank DPI: 0.177
Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. POOR DENSITY IS PRESENT FOR RESIDUES A57, A58, A59, A60, A61, A336, A337, A338, A339, A340, B59, B60, B61, B82, B83, B338, B339, B340. FINAL ...Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. POOR DENSITY IS PRESENT FOR RESIDUES A57, A58, A59, A60, A61, A336, A337, A338, A339, A340, B59, B60, B61, B82, B83, B338, B339, B340. FINAL STRUCTURE HAS NO RESIDUES IN THE DISALLOWED REGION OF THE RAMACHANDRAN PLOT AS DEFINED IN THE CCP4 PROCHECK PROGRAM.
RfactorNum. reflection% reflectionSelection details
Rfree0.2631 2602 5.04 %RANDOM
Rwork0.2074 ---
obs0.2102 51587 94.43 %-
Displacement parametersBiso mean: 40.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.356 Å20 Å2-0.1565 Å2
2---0.0413 Å20 Å2
3----0.3148 Å2
Refine analyzeLuzzati coordinate error obs: 0.277 Å
Refinement stepCycle: LAST / Resolution: 1.9→15.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5466 0 194 387 6047
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015959HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.148148HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2019SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes170HARMONIC2
X-RAY DIFFRACTIONt_gen_planes880HARMONIC5
X-RAY DIFFRACTIONt_it5959HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion19.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion749SEMIHARMONIC5
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_contact7153SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3393 200 5.29 %
Rwork0.2986 3579 -
all0.3007 3779 -
obs--94.43 %

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