← Back to search
1vdv

Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form

Method: X-RAY DIFFRACTION
▼

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

Xanthine dehydrogenase/oxidase

OrganismNot specified

UniProt P80457

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 × 4 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 DIOXOTHIOMOLYBDENUM(VI) ION × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 1-[3-CYANO-4-(NEOPENTYLOXY)PHENYL]-1H-PYRAZOLE-4-CARBOXYLIC ACID × 2 GLYCEROL × 21 ACETIC ACID × 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1fo4 1n5x 1v97 1vdv 3am9 3amz 3ax7 3ax9 3bdj 3una 3unc 3uni

13 assemblies; showing the first 12

Homotetramer

None

Other homooligomers
1fiq 3b9j 3b9j 3etr 3etr 3etr 3eub 3eub 3nrz 3ns1 3nvv 3nvw

15 assemblies; showing the first 12

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name XDH_BOVIN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–1332； UniProt 1–1331 Author chain B； PDBConstruct 2–1332； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1vdv
Deposition date deposition_date2004-03-25
Structure title titleBovine Milk Xanthine Dehydrogenase Y-700 Bound Form
Keywords keywordsxanthine oxidoreductase, Y-700, inhibitor, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
▼

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.

1vdv__assembly_1__model_1

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

Download this curve (.dat)

1vdv__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1vdv__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）45.06 Å
Rg (electron density)45.32 Å
Total Rg45.38 Å
Atom count20491
Residues2595
Excluded volume366230 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1vdv__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (10)

▼

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1vdva1
Class classa — All alpha proteins
Fold Fold folda.56 — CO dehydrogenase ISP C-domain like
Superfamily Superfamily superfamilya.56.1 — CO dehydrogenase ISP C-domain like
Family Family familya.56.1.1 — CO dehydrogenase ISP C-domain like
Domain ID domain_idd1vdva2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.4 — 2Fe-2S ferredoxin-like
Family Family familyd.15.4.2 — 2Fe-2S ferredoxin domains from multidomain proteins
Domain ID domain_idd1vdva3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.41 — alpha/beta-Hammerhead
Superfamily Superfamily superfamilyd.41.1 — CO dehydrogenase molybdoprotein N-domain-like
Family Family familyd.41.1.1 — CO dehydrogenase molybdoprotein N-domain-like
Domain ID domain_idd1vdva4
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.87 — CO dehydrogenase flavoprotein C-domain-like
Superfamily Superfamily superfamilyd.87.2 — CO dehydrogenase flavoprotein C-terminal domain-like
Family Family familyd.87.2.1 — CO dehydrogenase flavoprotein C-terminal domain-like
Domain ID domain_idd1vdva5
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.133 — Molybdenum cofactor-binding domain
Superfamily Superfamily superfamilyd.133.1 — Molybdenum cofactor-binding domain
Family Family familyd.133.1.1 — Molybdenum cofactor-binding domain
Domain ID domain_idd1vdva6
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.145 — FAD-binding/transporter-associated domain-like
Superfamily Superfamily superfamilyd.145.1 — FAD-binding/transporter-associated domain-like
Family Family familyd.145.1.3 — CO dehydrogenase flavoprotein N-terminal domain-like
Domain ID domain_idd1vdvb1
Class classa — All alpha proteins
Fold Fold folda.56 — CO dehydrogenase ISP C-domain like
Superfamily Superfamily superfamilya.56.1 — CO dehydrogenase ISP C-domain like
Family Family familya.56.1.1 — CO dehydrogenase ISP C-domain like
Domain ID domain_idd1vdvb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.4 — 2Fe-2S ferredoxin-like
Family Family familyd.15.4.2 — 2Fe-2S ferredoxin domains from multidomain proteins
Domain ID domain_idd1vdvb3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.41 — alpha/beta-Hammerhead
Superfamily Superfamily superfamilyd.41.1 — CO dehydrogenase molybdoprotein N-domain-like
Family Family familyd.41.1.1 — CO dehydrogenase molybdoprotein N-domain-like
Domain ID domain_idd1vdvb4
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.87 — CO dehydrogenase flavoprotein C-domain-like
Superfamily Superfamily superfamilyd.87.2 — CO dehydrogenase flavoprotein C-terminal domain-like
Family Family familyd.87.2.1 — CO dehydrogenase flavoprotein C-terminal domain-like
Domain ID domain_idd1vdvb5
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.133 — Molybdenum cofactor-binding domain
Superfamily Superfamily superfamilyd.133.1 — Molybdenum cofactor-binding domain
Family Family familyd.133.1.1 — Molybdenum cofactor-binding domain
Domain ID domain_idd1vdvb6
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.145 — FAD-binding/transporter-associated domain-like
Superfamily Superfamily superfamilyd.145.1 — FAD-binding/transporter-associated domain-like
Family Family familyd.145.1.3 — CO dehydrogenase flavoprotein N-terminal domain-like

CATH v4.4 (20 domains)

Domain ID domain_id1vdvA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily30 — Beta-grasp domain
Domain ID domain_id1vdvA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily120 — [2Fe-2S]-binding domain
Domain ID domain_id1vdvA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2
Domain ID domain_id1vdvA04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1vdvA05
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily50 — CO dehydrogenase flavoprotein, C-terminal domain
Domain ID domain_id1vdvA06
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
Domain ID domain_id1vdvA07
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily50 — Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead
Domain ID domain_id1vdvA08
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
Domain ID domain_id1vdvA09
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
Domain ID domain_id1vdvA10
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
Domain ID domain_id1vdvB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily30 — Beta-grasp domain
Domain ID domain_id1vdvB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily120 — [2Fe-2S]-binding domain
Domain ID domain_id1vdvB03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2
Domain ID domain_id1vdvB04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1vdvB05
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily50 — CO dehydrogenase flavoprotein, C-terminal domain
Domain ID domain_id1vdvB06
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
Domain ID domain_id1vdvB07
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily50 — Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead
Domain ID domain_id1vdvB08
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
Domain ID domain_id1vdvB09
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
Domain ID domain_id1vdvB10
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
▶

7. Citations (1)