6abu

Rat Xanthine oxidoreductase, NAD bound form

Method: X-RAY DIFFRACTION

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

Xanthine dehydrogenase/oxidase

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 URIC ACID × 2 BICARBONATE ION × 2 FE2/S2 (INORGANIC) CLUSTER × 4 FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XDH_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1331； UniProt 1–1331 Author chain B； PDBConstruct 1–1331； UniProt 1–1331

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	6abu
Deposition date deposition_date	2018-07-24
Structure title title	Rat Xanthine oxidoreductase, NAD bound form
Keywords keywords	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.

6abu__assembly_1__model_1

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

Download this curve (.dat)

6abu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6abu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.17 Å
Rg (electron density)	45.37 Å
Total Rg	45.47 Å
Atom count	20251
Residues	2595
Excluded volume	361050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6abu__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 (7)

Entity 1 Entity 1 polymer

Description description	Xanthine dehydrogenase/oxidase
Molecular weight formula_weight	146414.4 kDa
EC 编号 ec_number	1.17.1.4,1.17.3.2
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	21843

MTADELVFFVNGKKVVEKNADPETTLLVYLRRKLGLCGTKLGCGEGGCGACTVMISKYDRLQNKIVHFSVNACLAPICSLHHVAVTTVEGIGNTQKLHPVQERIARSHGSQCGFCTPGIVMSMYTLLRNQPEPTVEEIENAFQGNLCRCTGYRPILQGFRTFAKDGGCCGGSGNNPNCCMNQTKDQTVSLSPSLFNPEDFKPLDPTQEPIFPPELLRLKDTPQKKLRFEGERVTWIQASTMEELLDLKAQHPDAKLVVGNTEIGIEMKFKNMLFPLIVCPAWIPELNSVVHGPEGISFGASCPLSLVESVLAEEIAKLPEQKTEVFRGVMEQLRWFAGKQVKSVASIGGNIITASPISDLNPVFMASGAKLTLVSRGTRRTVRMDHTFFPGYRKTLLRPEEILLSIEIPYSKEGEFFSAFKQASRREDDIAKVTSGMRVLFKPGTIEVQELSLCFGGMADRTISALKTTPKQLSKSWNEELLQSVCAGLAEELQLAPDAPGGMVEFRRTLTLSFFFKFYLTVLQKLGRADLEDMCGKLDPTFASATLLFQKDPPANVQLFQEVPKDQSEEDMVGRPLPHLAANMQASGEAVYCDDIPRYENELSLRLVTSTRAHAKITSIDTSEAKKVPGFVCFLTAEDVPNSNATGLFNDETVFAKDEVTCVGHIIGAVVADTPEHAQRAARGVKITYEDLPAIITIQDAINNNSFYGSEIKIEKGDLKKGFSEADNVVSGELYIGGQEHFYLETNCTIAVPKGEAGEMELFVSTQNTMKTQSFVAKMLGVPDNRIVVRVKRMGGGFGGKETRSTVVSTALALAAHKTGRPVRCMLDRDEDMLITGGRHPFLAKYKVGFMKTGTVVALEVAHFSNGGNTEDLSRSIMERALFHMDNAYKIPNIRGTGRICKTNLPSNTAFRGFGGPQGMLIAEYWMSEVAITCGLPAEEVRRKNMYKEGDLTHFNQKLEGFTLPRCWDECIASSQYLARKREVEKFNRENCWKKRGLCIIPTKFGISFTLPFLNQGGALVHVYTDGSVLLTHGGTEMGQGLHTKMVQVASRALKIPTSKIHISETSTNTVPNTSPTAASASADLNGQGVYEACQTILKRLEPFKKKKPTGPWEAWVMDAYTSAVSLSATGFYKTPNLGYSFETNSGNPFHYFSYGVACSEVEIDCLTGDHKNLRTDIVMDVGSSLNPAIDIGQVEGAFVQGLGLFTMEELHYSPEGSLHTRGPSTYKIPAFGSIPIEFRVSLLRDCPNKRAIYASKAVGEPPLFLASSIFFAIKDAIRAARAQHGDNAKQLFQLDSPATPEKIRNACVDQFTTLCVTGVPENCKSWSVRI

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	URIC ACID
Molecular weight formula_weight	168.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	BICARBONATE ION
Molecular weight formula_weight	61.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 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 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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1592

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6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id	6abuA01
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	6abuA02
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	6abuA03
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	6abuA05
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	6abuA06
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	6abuA07
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	6abuA08
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	6abuA09
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	6abuA10
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	6abuB01
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	6abuB02
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	6abuB03
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	6abuB05
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	6abuB06
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	6abuB07
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	6abuB08
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	6abuB09
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	6abuB10
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

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Unit-cell length a length_a	98.353 Å
Unit-cell length b length_b	137.663 Å
Unit-cell length c length_c	221.969 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.770 Å
Low-resolution limit resolution_low	30.570 Å
R factor r_factor	0.2008
R_work r_work	0.1989
R_free r_free	0.2366

Rat Xanthine oxidoreductase, NAD bound form

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

6abu__assembly_1__model_1

6abu__assembly_1__model_1 | I(q)

6abu__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

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 water

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (2)

Rat Xanthine oxidoreductase, NAD bound form

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

6abu__assembly_1__model_1

6abu__assembly_1__model_1 | I(q)

6abu__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

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 water

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (2)