3bdj

Crystal Structure of Bovine Milk Xanthine Dehydrogenase with a Covalently Bound Oxipurinol Inhibitor

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Xanthine dehydrogenase/oxidase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 2 FE2/S2 (INORGANIC) CLUSTER × 4 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 × 2 Oxo(sulfanyl)molybdenum(IV) ION × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 Oxypurinol × 2 GLYCEROL × 7 CARBONATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XDH_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1332； UniProt 1–1332 Author chain B； PDBConstruct 1–1332； UniProt 1–1332

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3bdj
Deposition date deposition_date	2007-11-14
Structure title title	Crystal Structure of Bovine Milk Xanthine Dehydrogenase with a Covalently Bound Oxipurinol Inhibitor
Keywords keywords	;OXYPURINOL, OXIPURINOL, ALLOXANTHINE, ALLOPURINOL, COVALENTLY BOUND INHIBITOR, XANTHINE OXIDASE, XANTHINE OXIDOREDUCTASE, XANTHINE DEHYDROGENASE, FAD, FLAVOPROTEIN, IRON-SULFUR, MOLYBDOPTERIN, PEROXISOME, OXIDOREDUCTASE ;; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3bdj__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3bdj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bdj__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	44.86 Å
Rg (electron density)	45.16 Å
Total Rg	45.22 Å
Atom count	20232
Residues	2572
Excluded volume	361310 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bdj__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	Xanthine dehydrogenase/oxidase
Molecular weight formula_weight	146993.1 kDa
EC 编号 ec_number	1.17.3.2, 1.17.1.4
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	21626

MTADELVFFVNGKKVVEKNADPETTLLAYLRRKLGLRGTKLGCGEGGCGACTVMLSKYDRLQDKIIHFSANACLAPICTLHHVAVTTVEGIGSTKTRLHPVQERIAKSHGSQCGFCTPGIVMSMYTLLRNQPEPTVEEIEDAFQGNLCRCTGYRPILQGFRTFAKNGGCCGGNGNNPNCCMNQKKDHTVTLSPSLFNPEEFMPLDPTQEPIFPPELLRLKDVPPKQLRFEGERVTWIQASTLKELLDLKAQHPEAKLVVGNTEIGIEMKFKNQLFPMIICPAWIPELNAVEHGPEGISFGAACALSSVEKTLLEAVAKLPTQKTEVFRGVLEQLRWFAGKQVKSVASLGGNIITASPISDLNPVFMASGTKLTIVSRGTRRTVPMDHTFFPSYRKTLLGPEEILLSIEIPYSREDEFFSAFKQASRREDDIAKVTCGMRVLFQPGSMQVKELALCYGGMADRTISALKTTQKQLSKFWNEKLLQDVCAGLAEELSLSPDAPGGMIEFRRTLTLSFFFKFYLTVLKKLGKDSKDKCGKLDPTYTSATLLFQKHPPANIQLFQEVPNGQSKEDTVGRPLPHLAAAMQASGEAVYCDDIPRYENELFLRLVTSTRAHAKIKSIDVSEAQKVPGFVCFLSADDIPGSNETGLFNDETVFAKDTVTCVGHIIGAVVADTPEHAERAAHVVKVTYEDLPAIITIEDAIKNNSFYGSELKIEKGDLKKGFSEADNVVSGELYIGGQDHFYLETHCTIAIPKGEEGEMELFVSTQNAMKTQSFVAKMLGVPVNRILVRVKRMGGGFGGKETRSTLVSVAVALAAYKTGHPVRCMLDRNEDMLITGGRHPFLARYKVGFMKTGTIVALEVDHYSNAGNSRDLSHSIMERALFHMDNCYKIPNIRGTGRLCKTNLSSNTAFRGFGGPQALFIAENWMSEVAVTCGLPAEEVRWKNMYKEGDLTHFNQRLEGFSVPRCWDECLKSSQYYARKSEVDKFNKENCWKKRGLCIIPTKFGISFTVPFLNQAGALIHVYTDGSVLVSHGGTEMGQGLHTKMVQVASKALKIPISKIYISETSTNTVPNSSPTAASVSTDIYGQAVYEACQTILKRLEPFKKKNPDGSWEDWVMAAYQDRVSLSTTGFYRTPNLGYSFETNSGNAFHYFTYGVACSEVEIDCLTGDHKNLRTDIVMDVGSSLNPAIDIGQVEGAFVQGLGLFTLEELHYSPEGSLHTRGPSTYKIPAFGSIPTEFRVSLLRDCPNKKAIYASKAVGEPPLFLGASVFFAIKDAIRAARAQHTNNNTKELFRLDSPATPEKIRNACVDKFTTLCVTGAPGNCKPWSLRV

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	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
Molecular weight formula_weight	395.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	Oxo(sulfanyl)molybdenum(IV) ION
Molecular weight formula_weight	145.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	Oxypurinol
Molecular weight formula_weight	152.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 9 Entity 9 non-polymer

Description description	CARBONATE ION
Molecular weight formula_weight	60.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1394

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3bdja1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.2 — 2Fe-2S ferredoxin domains from multidomain proteins

Domain ID domain_id	d3bdja2
Class class	a — All alpha proteins
Fold Fold fold	a.56 — CO dehydrogenase ISP C-domain like
Superfamily Superfamily superfamily	a.56.1 — CO dehydrogenase ISP C-domain like
Family Family family	a.56.1.1 — CO dehydrogenase ISP C-domain like

Domain ID domain_id	d3bdja3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.145 — FAD-binding/transporter-associated domain-like
Superfamily Superfamily superfamily	d.145.1 — FAD-binding/transporter-associated domain-like
Family Family family	d.145.1.3 — CO dehydrogenase flavoprotein N-terminal domain-like

Domain ID domain_id	d3bdja4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
Superfamily Superfamily superfamily	d.87.2 — CO dehydrogenase flavoprotein C-terminal domain-like
Family Family family	d.87.2.1 — CO dehydrogenase flavoprotein C-terminal domain-like

Domain ID domain_id	d3bdja5
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.41 — alpha/beta-Hammerhead
Superfamily Superfamily superfamily	d.41.1 — CO dehydrogenase molybdoprotein N-domain-like
Family Family family	d.41.1.1 — CO dehydrogenase molybdoprotein N-domain-like

Domain ID domain_id	d3bdja6
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.133 — Molybdenum cofactor-binding domain
Superfamily Superfamily superfamily	d.133.1 — Molybdenum cofactor-binding domain
Family Family family	d.133.1.1 — Molybdenum cofactor-binding domain

Domain ID domain_id	d3bdjb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.2 — 2Fe-2S ferredoxin domains from multidomain proteins

Domain ID domain_id	d3bdjb2
Class class	a — All alpha proteins
Fold Fold fold	a.56 — CO dehydrogenase ISP C-domain like
Superfamily Superfamily superfamily	a.56.1 — CO dehydrogenase ISP C-domain like
Family Family family	a.56.1.1 — CO dehydrogenase ISP C-domain like

Domain ID domain_id	d3bdjb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.145 — FAD-binding/transporter-associated domain-like
Superfamily Superfamily superfamily	d.145.1 — FAD-binding/transporter-associated domain-like
Family Family family	d.145.1.3 — CO dehydrogenase flavoprotein N-terminal domain-like

Domain ID domain_id	d3bdjb4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
Superfamily Superfamily superfamily	d.87.2 — CO dehydrogenase flavoprotein C-terminal domain-like
Family Family family	d.87.2.1 — CO dehydrogenase flavoprotein C-terminal domain-like

Domain ID domain_id	d3bdjb5
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.41 — alpha/beta-Hammerhead
Superfamily Superfamily superfamily	d.41.1 — CO dehydrogenase molybdoprotein N-domain-like
Family Family family	d.41.1.1 — CO dehydrogenase molybdoprotein N-domain-like

Domain ID domain_id	d3bdjb6
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.133 — Molybdenum cofactor-binding domain
Superfamily Superfamily superfamily	d.133.1 — Molybdenum cofactor-binding domain
Family Family family	d.133.1.1 — Molybdenum cofactor-binding domain

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Unit-cell length a length_a	166.517 Å
Unit-cell length b length_b	124.074 Å
Unit-cell length c length_c	148.797 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	19.960 Å
R factor r_factor	0.1910
R_work r_work	0.1910
R_free r_free	0.2240

Crystal Structure of Bovine Milk Xanthine Dehydrogenase with a Covalently Bound Oxipurinol Inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Xanthine dehydrogenase/oxidase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3bdj__assembly_1__model_1

3bdj__assembly_1__model_1 | I(q)

3bdj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

7. Citations (5)

Crystal Structure of Bovine Milk Xanthine Dehydrogenase with a Covalently Bound Oxipurinol Inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Xanthine dehydrogenase/oxidase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3bdj__assembly_1__model_1

3bdj__assembly_1__model_1 | I(q)

3bdj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

7. Citations (5)