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- PDB-3bdj: Crystal Structure of Bovine Milk Xanthine Dehydrogenase with a Co... -

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Basic information

Entry
Database: PDB / ID: 3bdj
TitleCrystal Structure of Bovine Milk Xanthine Dehydrogenase with a Covalently Bound Oxipurinol Inhibitor
ComponentsXanthine dehydrogenase/oxidase
KeywordsOXIDOREDUCTASE / OXYPURINOL / OXIPURINOL / ALLOXANTHINE / ALLOPURINOL / COVALENTLY BOUND INHIBITOR / XANTHINE OXIDASE / XANTHINE OXIDOREDUCTASE / XANTHINE DEHYDROGENASE / FAD / FLAVOPROTEIN / IRON-SULFUR / MOLYBDOPTERIN / PEROXISOME
Function / homology
Function and homology information


xanthine dehydrogenase complex / xanthine dehydrogenase / xanthine oxidase / xanthine oxidase activity / xanthine catabolic process / xanthine dehydrogenase activity / molybdenum ion binding / molybdopterin cofactor binding / FAD binding / 2 iron, 2 sulfur cluster binding ...xanthine dehydrogenase complex / xanthine dehydrogenase / xanthine oxidase / xanthine oxidase activity / xanthine catabolic process / xanthine dehydrogenase activity / molybdenum ion binding / molybdopterin cofactor binding / FAD binding / 2 iron, 2 sulfur cluster binding / peroxisome / flavin adenine dinucleotide binding / iron ion binding / protein homodimerization activity / extracellular space
Similarity search - Function
Xanthine dehydrogenase, small subunit / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / CO dehydrogenase flavoprotein C-terminal domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde oxidase/xanthine dehydrogenase ...Xanthine dehydrogenase, small subunit / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / CO dehydrogenase flavoprotein C-terminal domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde oxidase/xanthine dehydrogenase / Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding / Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / [2Fe-2S]-binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily / [2Fe-2S] binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / FAD-binding, type PCMH, subdomain 1 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / 2Fe-2S iron-sulfur cluster binding domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
Oxypurinol / CARBONATE ION / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Oxo(sulfanyl)molybdenum(IV) ION / Chem-MTE / Xanthine dehydrogenase/oxidase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEger, B.T. / Okamoto, K. / Nishino, T. / Pai, E.F. / Nishino, T.
Citation
Journal: Nucleosides Nucleotides Nucleic Acids / Year: 2008
Title: Mechanism of inhibition of xanthine oxidoreductase by allopurinol: crystal structure of reduced bovine milk xanthine oxidoreductase bound with oxipurinol.
Authors: Okamoto, K. / Eger, B.T. / Nishino, T. / Pai, E.F. / Nishino, T.
#1: Journal: Structure / Year: 2002
Title: Crystal Structures of the Active and Alloxanthine-inhibited forms of Xanthine Dehydrogenase from Rhodobacter Capsulatusa
Authors: Truglio, J.J. / Theis, K. / Leimkuhler, S. / Rappa, R. / Rajagopalan, K.V. / Kisker, C.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: The Crystal Structure of Xanthine Oxidoreductase during catalysis: Implications for reaction mechanism and enzyme inhibition
Authors: Okamoto, K. / Matsumoto, K. / Hille, R. / Eger, B.T. / Pai, E.F. / Nishino, T.
#3: Journal: J.PHARMACOL.EXP.THER. / Year: 2004
Title: Y-700[1-[3-CYANO-4-(2,2-DIMETHYLPROPOXY)PHENYL]-1H-PYRAZOLE-4-CARBOXYLIC ACID]: A Potent Xanthine Oxidoreductase Inhibitor with Hepatic excretion
Authors: Fukunari, A. / Okamoto, K. / Nishino, T. / Eger, B.T. / Pai, E.F. / Kamezawa, M. / Yamada, I. / Kato, N.
#4: Journal: J.Biol.Chem. / Year: 2003
Title: An extremely potent inhibitor of Xanthine Oxidoreductase Crystal Structure of the enzyme-inhibitor complex and Mechanism of Inhibition
Authors: Okamoto, K. / Eger, B.T. / Nishino, T. / Kondo, S. / Pai, E.F. / Nishino, T.
History
DepositionNov 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Sep 10, 2014Group: Non-polymer description
Revision 1.3Aug 30, 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xanthine dehydrogenase/oxidase
B: Xanthine dehydrogenase/oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,49025
Polymers293,9862
Non-polymers4,50423
Water25,1131394
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.517, 124.074, 148.797
Angle α, β, γ (deg.)90.00, 91.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Xanthine dehydrogenase/oxidase


Mass: 146993.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: P80457, xanthine oxidase, xanthine dehydrogenase

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Non-polymers , 9 types, 1417 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-MTE / PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER


Mass: 395.352 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O6PS2
#5: Chemical ChemComp-MOW / Oxo(sulfanyl)molybdenum(IV) ION


Mass: 145.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HMoOS
#6: 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
#7: Chemical ChemComp-141 / Oxypurinol / Alloxanthine / Oxipurinol


Mass: 152.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O2 / Comment: inhibitor*YM
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1394 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsUNP ENTRY P80457 HAS A CONFLICT ASP TO HIS AT RESIDUE 552

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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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 4000, DTT, GLYCEROL, KPI, NAPPI, EDTA, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 204186 / Num. obs: 192610 / % possible obs: 94.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.2 / % possible all: 80.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
EPMRphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1fo4

1fo4


Resolution: 2→19.96 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2299 -RANDOM
Rwork0.191 ---
obs0.191 182241 89.6 %-
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å20 Å20.65 Å2
2---4.88 Å20 Å2
3---6.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19982 0 250 1394 21626
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.308 324 -
Rwork0.286 --
obs--75.2 %

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