3eub

Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine

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 6	FE2/S2 (INORGANIC) CLUSTER × 4 FLAVIN-ADENINE DINUCLEOTIDE × 2 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 HYDROXY(DIOXO)MOLYBDENUM × 2 XANTHINE × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	FE2/S2 (INORGANIC) CLUSTER × 4 FLAVIN-ADENINE DINUCLEOTIDE × 2 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 HYDROXY(DIOXO)MOLYBDENUM × 2 XANTHINE × 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, 2, 3
Chains and sequence ranges	Author chain 2； PDBConstruct 1–165； UniProt 1–165 Author chain A； PDBConstruct 1–165； UniProt 1–165 Author chain J； PDBConstruct 1–165； UniProt 1–165 Author chain S； PDBConstruct 1–165； UniProt 1–165 Author chain 3； PDBConstruct 1–305； UniProt 224–528 Author chain B； PDBConstruct 1–305； UniProt 224–528 Author chain K； PDBConstruct 1–305； UniProt 224–528 Author chain T； PDBConstruct 1–305； UniProt 224–528 Author chain 4； PDBConstruct 1–762； UniProt 571–1332 Author chain C； PDBConstruct 1–762； UniProt 571–1332 Author chain L； PDBConstruct 1–762； UniProt 571–1332 Author chain U； PDBConstruct 1–762； UniProt 571–1332

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	3eub
Deposition date deposition_date	2008-10-09
Structure title title	Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine
Keywords keywords	;enzyme catalysis, desulfo, substrate orientation, xanthine, FAD, Flavoprotein, Iron, Iron-sulfur, Metal-binding, Molybdenum, NAD, Oxidoreductase, Peroxisome ;; 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.

3eub__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3eub__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3eub__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	44.74 Å
Rg (electron density)	45.03 Å
Total Rg	45.10 Å
Atom count	19060
Residues	2436
Excluded volume	340050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3eub__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3eub__assembly_2__model_1`	hexameric （6）	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 (8)

Entity 1 Entity 1 polymer

Description description	Xanthine dehydrogenase/oxidase
Molecular weight formula_weight	18134.1 kDa
EC 编号 ec_number	1.17.1.4, 1.17.3.2
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,J,S,2
Atom count atom_count	38070

MTADELVFFVNGKKVVEKNADPETTLLAYLRRKLGLRGTKLGCGEGGCGACTVMLSKYDRLQDKIIHFSANACLAPICTLHHVAVTTVEGIGSTKTRLHPVQERIAKSHGSQCGFCTPGIVMSMYTLLRNQPEPTVEEIEDAFQGNLCRCTGYRPILQGFRTFAK

Entity 2 Entity 2 polymer

Description description	Xanthine dehydrogenase/oxidase
Molecular weight formula_weight	34024.6 kDa
EC 编号 ec_number	1.17.1.4, 1.17.3.2
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,K,T,3

PKQLRFEGERVTWIQASTLKELLDLKAQHPEAKLVVGNTEIGIEMKFKNQLFPMIICPAWIPELNAVEHGPEGISFGAACALSSVEKTLLEAVAKLPTQKTEVFRGVLEQLRWFAGKQVKSVASLGGNIITASPISDLNPVFMASGTKLTIVSRGTRRTVPMDHTFFPSYRKTLLGPEEILLSIEIPYSREDEFFSAFKQASRREDDIAKVTCGMRVLFQPGSMQVKELALCYGGMADRTISALKTTQKQLSKFWNEKLLQDVCAGLAEELSLSPDAPGGMIEFRRTLTLSFFFKFYLTVLKKLG

Entity 3 Entity 3 polymer

Description description	Xanthine dehydrogenase/oxidase
Molecular weight formula_weight	83835.3 kDa
EC 编号 ec_number	1.17.1.4, 1.17.3.2
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,L,U,4

DTVGRPLPHLAAAMQASGEAVYCDDIPRYENELFLRLVTSTRAHAKIKSIDVSEAQKVPGFVCFLSADDIPGSNETGLFNDETVFAKDTVTCVGHIIGAVVADTPEHAERAAHVVKVTYEDLPAIITIEDAIKNNSFYGSELKIEKGDLKKGFSEADNVVSGELYIGGQDHFYLETHCTIAIPKGEEGEMELFVSTQNAMKTQSFVAKMLGVPVNRILVRVKRMGGGFGGKETRSTLVSVAVALAAYKTGHPVRCMLDRNEDMLITGGRHPFLARYKVGFMKTGTIVALEVDHYSNAGNSRDLSHSIMERALFHMDNCYKIPNIRGTGRLCKTNLSSNTAFRGFGGPQALFIAENWMSEVAVTCGLPAEEVRWKNMYKEGDLTHFNQRLEGFSVPRCWDECLKSSQYYARKSEVDKFNKENCWKKRGLCIIPTKFGISFTVPFLNQAGALIHVYTDGSVLVSHGGTEMGQGLHTKMVQVASKALKIPISKIYISETSTNTVPNSSPTAASVSTDIYGQAVYEACQTILKRLEPFKKKNPDGSWEDWVMAAYQDRVSLSTTGFYRTPNLGYSFETNSGNAFHYFTYGVACSEVEIDCLTGDHKNLRTDIVMDVGSSLNPAIDIGQVEGAFVQGLGLFTLEELHYSPEGSLHTRGPSTYKIPAFGSIPTEFRVSLLRDCPNKKAIYASKAVGEPPLFLGASVFFAIKDAIRAARAQHTNNNTKELFRLDSPATPEKIRNACVDKFTTLCVTGAPGNCKPWSLRV

Entity 4 Entity 4 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 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	4

Entity 7 Entity 7 non-polymer

Description description	HYDROXY(DIOXO)MOLYBDENUM
Molecular weight formula_weight	144.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	XANTHINE
Molecular weight formula_weight	152.1 kDa
Source method src_method	syn
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 64 domains

SCOP 2.08 (24 domains)

Domain ID domain_id	d3eub21
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	d3eub22
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	d3eub31
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	d3eub32
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.87.2.0 — automated matches

Domain ID domain_id	d3eub41
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.41.1.0 — automated matches

Domain ID domain_id	d3eub42
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	d3euba1
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	d3euba2
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	d3eubb1
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	d3eubb2
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.87.2.0 — automated matches

Domain ID domain_id	d3eubc1
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.41.1.0 — automated matches

Domain ID domain_id	d3eubc2
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	d3eubj1
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	d3eubj2
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	d3eubk1
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	d3eubk2
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.87.2.0 — automated matches

Domain ID domain_id	d3eubl1
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.41.1.0 — automated matches

Domain ID domain_id	d3eubl2
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	d3eubs1
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	d3eubs2
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	d3eubt1
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	d3eubt2
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.87.2.0 — automated matches

Domain ID domain_id	d3eubu1
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.41.1.0 — automated matches

Domain ID domain_id	d3eubu2
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

CATH v4.4 (40 domains)

Domain ID domain_id	3eub201
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	30 — Beta-grasp domain

Domain ID domain_id	3eub202
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	120 — [2Fe-2S]-binding domain

Domain ID domain_id	3eub301
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

Domain ID domain_id	3eub302
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3eub303
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	50 — CO dehydrogenase flavoprotein, C-terminal domain

Domain ID domain_id	3eub401
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily	50 — Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead

Domain ID domain_id	3eub402
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	3eub403
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	3eub404
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	3eub405
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	3eubA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	30 — Beta-grasp domain

Domain ID domain_id	3eubA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	120 — [2Fe-2S]-binding domain

Domain ID domain_id	3eubB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

Domain ID domain_id	3eubB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3eubB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	50 — CO dehydrogenase flavoprotein, C-terminal domain

Domain ID domain_id	3eubC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily	50 — Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead

Domain ID domain_id	3eubC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	3eubC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	3eubC04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	3eubC05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	3eubJ01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	30 — Beta-grasp domain

Domain ID domain_id	3eubJ02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	120 — [2Fe-2S]-binding domain

Domain ID domain_id	3eubK01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

Domain ID domain_id	3eubK02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3eubK03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	50 — CO dehydrogenase flavoprotein, C-terminal domain

Domain ID domain_id	3eubL01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily	50 — Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead

Domain ID domain_id	3eubL02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	3eubL03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	3eubL04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	3eubL05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	3eubS01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	30 — Beta-grasp domain

Domain ID domain_id	3eubS02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	120 — [2Fe-2S]-binding domain

Domain ID domain_id	3eubT01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

Domain ID domain_id	3eubT02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3eubT03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	50 — CO dehydrogenase flavoprotein, C-terminal domain

Domain ID domain_id	3eubU01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily	50 — Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead

Domain ID domain_id	3eubU02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	3eubU03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	3eubU04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	3eubU05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

▶

Unit-cell length a length_a	73.298 Å
Unit-cell length b length_b	133.176 Å
Unit-cell length c length_c	142.633 Å
Unit-cell angle α angle_alpha	96.88 °
Unit-cell angle β angle_beta	93.11 °
Unit-cell angle γ angle_gamma	90.02 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	33.080 Å
R factor r_factor	0.2170
R_work r_work	0.2140
R_free r_free	0.2680

Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine

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

3eub__assembly_2__model_1

3eub__assembly_2__model_1 | I(q)

3eub__assembly_2__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer 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

6. Fold Classification (SCOP + CATH) 64 domains

SCOP 2.08 (24 domains)

CATH v4.4 (40 domains)

7. Citations (1)

Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine

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

3eub__assembly_2__model_1

3eub__assembly_2__model_1 | I(q)

3eub__assembly_2__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer 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

6. Fold Classification (SCOP + CATH) 64 domains

SCOP 2.08 (24 domains)

CATH v4.4 (40 domains)

7. Citations (1)