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- PDB-4qfd: Co-crystal structure of compound 2 (3-(7-hydroxy-2-oxo-4-phenyl-2... -

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Basic information

Entry
Database: PDB / ID: 4qfd
TitleCo-crystal structure of compound 2 (3-(7-hydroxy-2-oxo-4-phenyl-2H-chromen-6-yl)propanoic acid) and FAD bound to human DAAO at 2.85A
ComponentsD-amino-acid oxidase
Keywordsoxidoreductase/oxidoreductase inhibitor / OXIDASE / OXIDOREDUCTASE / DAAO / D-AMINO ACID OXIDASE / D-serine competitive / schizophrenia / NMDA receptor / oxidoreductase-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-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
Chem-31R / FLAVIN-ADENINE DINUCLEOTIDE / D-amino-acid oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsEdwards, T.E. / Chun, L. / Arakaki, T.L.
CitationJournal: Biosci.Rep. / Year: 2014
Title: Novel human D-amino acid oxidase inhibitors stabilize an active-site lid-open conformation.
Authors: Terry-Lorenzo, R.T. / Chun, L.E. / Brown, S.P. / Heffernan, M.L. / Fang, Q.K. / Orsini, M.A. / Pollegioni, L. / Hardy, L.W. / Spear, K.L. / Large, T.H.
History
DepositionMay 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Structure summary
Revision 1.2Nov 26, 2014Group: Database references
Revision 1.3Dec 31, 2014Group: Database references
Revision 1.4Mar 4, 2015Group: Database references
Revision 1.5Mar 18, 2015Group: Database references
Revision 1.6Mar 25, 2015Group: Database references
Revision 1.7Jun 17, 2015Group: Database references
Revision 1.8Jul 15, 2015Group: Database references
Revision 1.9Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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)81,2808
Polymers79,0422
Non-polymers2,2386
Water25214
1
A: D-amino-acid oxidase
hetero molecules

A: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2808
Polymers79,0422
Non-polymers2,2386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area6160 Å2
ΔGint-64 kcal/mol
Surface area24630 Å2
MethodPISA
2
B: D-amino-acid oxidase
hetero molecules

B: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2808
Polymers79,0422
Non-polymers2,2386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area6470 Å2
ΔGint-59 kcal/mol
Surface area23910 Å2
MethodPISA
3
A: D-amino-acid oxidase
B: D-amino-acid oxidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)162,55916
Polymers158,0844
Non-polymers4,47512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area14940 Å2
ΔGint-138 kcal/mol
Surface area46230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.490, 86.490, 187.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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: DAMOX, DAO, DAO DAMOX / Production host: Escherichia coli (E. coli) / References: UniProt: P14920, D-amino-acid oxidase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-31R / 3-(7-hydroxy-2-oxo-4-phenyl-2H-chromen-6-yl)propanoic acid


Mass: 310.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H14O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.57 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: DAAO AT 2 MG/ML IN 50 MM SODIUM PHOSPHATE PH 6.6, 10 UM FAD INCUBATED WITH 5-FOLD EXCESS OF SEP-0374036 OVERNIGHT AT 277 K, CRYSTALLIZED AGAINST 13.6% PEG3350, 0.1 M TRIS PH 7.4, 150 MM ...Details: DAAO AT 2 MG/ML IN 50 MM SODIUM PHOSPHATE PH 6.6, 10 UM FAD INCUBATED WITH 5-FOLD EXCESS OF SEP-0374036 OVERNIGHT AT 277 K, CRYSTALLIZED AGAINST 13.6% PEG3350, 0.1 M TRIS PH 7.4, 150 MM POTASSIUM CITRATE TRIBASIC AND 20 MM GLYCEROL AS CRYO-PROTECTANT, CRYSTAL TRACKING ID 241709B5, UNIQUE PUCK ID XSS6-4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 19576 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 69.55 Å2 / Rmerge(I) obs: 0.069 / Χ2: 0.965 / Net I/σ(I): 21.76
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 3.2 / Num. measured obs: 1049 / Num. unique obs: 186 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.85 Å19.9 Å
Translation2.85 Å19.9 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3CUK

3cuk


Resolution: 2.85→19.91 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.873 / WRfactor Rfree: 0.2523 / WRfactor Rwork: 0.216 / FOM work R set: 0.7299 / SU B: 52.653 / SU ML: 0.433 / SU R Cruickshank DPI: 0.4135 / SU Rfree: 0.436 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1000 5.1 %RANDOM
Rwork0.248 ---
obs0.25 19539 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.16 Å2 / Biso mean: 85.56 Å2 / Biso min: 30.41 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å21.63 Å20 Å2
2--1.63 Å20 Å2
3----5.3 Å2
Refinement stepCycle: LAST / Resolution: 2.85→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4885 0 154 14 5053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195190
X-RAY DIFFRACTIONr_bond_other_d0.0020.024592
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.9697123
X-RAY DIFFRACTIONr_angle_other_deg0.751310470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6875628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74623.616224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53915688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6681524
X-RAY DIFFRACTIONr_chiral_restr0.0570.2779
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215893
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021261
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_it1.0663.1932539
X-RAY DIFFRACTIONr_mcbond_other1.0673.1932538
X-RAY DIFFRACTIONr_mcangle_it1.8494.7833158
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 71 -
Rwork0.341 1347 -
all-1418 -
obs--99.79 %
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)
10.8808-0.8529-1.30483.86991.94482.3165-0.54020.0041-0.0283-0.27750.39270.44280.29520.11320.14760.8428-0.1924-0.03120.23990.06760.4553-0.054-14.82616.776
21.70210.93750.72970.83111.15552.8157-0.5610.406-0.4413-0.16120.4392-0.2374-0.07250.22510.12170.7198-0.14750.26650.5178-0.20740.473232.924-9.91313.705
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 336
2X-RAY DIFFRACTION1A401 - 403
3X-RAY DIFFRACTION2B1 - 336
4X-RAY DIFFRACTION2B401 - 403

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