Structure of PDB 1vdv Chain A

Receptor sequence

>1vdvA (length=1299) Species: 9913 (Bos taurus)

ADELVFFVNGKKVVEKNADPETTLLAYLRRKLGLRGTKLGCGEGGCGACT
VMLSKYDRLQDKIIHFSANACLAPICTLHHVAVTTVEGIGSTKTRLHPVQ
ERIAKSHGSQCGFCTPGIVMSMYTLLRNQPEPTVEEIEDAFQGNLCRCTG
YRPILQGFRTFAKSPSLFNPEEFMPLDPTQEPIFPPELLRLKDVPPKQLR
FEGERVTWIQASTLKELLDLKAQHPEAKLVVGNTEIGIEMKFKNQLFPMI
ICPAWIPELNAVEHGPEGISFGAACALSSVEKTLLEAVAKLPTQKTEVFR
GVLEQLRWFAGKQVKSVASLGGNIITASPISDLNPVFMASGTKLTIVSRG
TRRTVPMDHTFFPSYRKTLLGPEEILLSIEIPYSREDEFFSAFKQASRRE
DDIAKVTCGMRVLFQPGSMQVKELALCYGGMADRTISALKTTQKQLSKFW
NEKLLQDVCAGLAEELSLSPDAPGGMIEFRRTLTLSFFFKFYLTVLKKLG
KDSKLDPTYTSATLLFQKHPPANIQLFQEVPNGQSKEDTVGRPLPHLAAA
MQASGEAVYCDDIPRYENELFLRLVTSTRAHAKIKSIDVSEAQKVPGFVC
FLSADDIPGSNETGLFNDETVFAKDTVTCVGHIIGAVVADTPEHAERAAH
VVKVTYEDLPAIITIEDAIKNNSFYGSELKIEKGDLKKGFSEADNVVSGE
LYIGGQDHFYLETHCTIAIPKGEEGEMELFVSTQNAMKTQSFVAKMLGVP
VNRILVRVKRMGGGFGGKETRSTLVSVAVALAAYKTGHPVRCMLDRNEDM
LITGGRHPFLARYKVGFMKTGTIVALEVDHYSNAGNSRDLSHSIMERALF
HMDNCYKIPNIRGTGRLCKTNLSSNTAFRGFGGPQALFIAENWMSEVAVT
CGLPAEEVRWKNMYKEGDLTHFNQRLEGFSVPRCWDECLKSSQYYARKSE
VDKFNKENCWKKRGLCIIPTKFGISFTVPFLNQAGALIHVYTDGSVLVSH
GGTEMGQGLHTKMVQVASKALKIPISKIYISETSTNTVPNSSPTAASVST
DIYGQAVYEACQTILKRLEPFKKKNPDGSWEDWVMAAYQDRVSLSTTGFY
RTPNLGYSFETNSGNAFHYFTYGVACSEVEIDCLTGDHKNLRTDIVMDVG
SSLNPAIDIGQVEGAFVQGLGLFTLEELHYSPEGSLHTRGPSTYKIPAFG
SIPTEFRVSLLRDCPNKKAIYASKAVGEPPLFLGASVFFAIKDAIRAARA
QHTNNNTKELFRLDSPATPEKIRNACVDKFTTLCVTGAPGNCKPWSLRV

3D structure

• PDB: 1vdv Y-700 [1-[3-Cyano-4-(2,2-dimethylpropoxy)phenyl]-1H-pyrazole-4-carboxylic acid]: a potent xanthine oxidoreductase inhibitor with hepatic excretion
• Chain: A
• Resolution: 1.98 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Q767 E802 R880 H884 R912 G1260 E1261
• Catalytic site (residue number reindexed from 1): Q734 E769 R847 H851 R879 G1227 E1228
• Enzyme Commision number: 1.17.1.4: xanthine dehydrogenase.
  1.17.3.2: xanthine oxidase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	CA	A	A867 S870 R871 S874 S907 N908	A834 S837 R838 S841 S874 N875
BS02	CA	A	H741 Y743 T836 G837	H708 Y710 T803 G804
BS03	FES	A	Q112 C113 G114 C116 C148 C150 L744	Q110 C111 G112 C114 C146 C148 L711
BS04	FES	A	G42 C43 G44 G46 C48 G49 C51 C73	G40 C41 G42 G44 C46 G47 C49 C71
BS05	FAD	A	E45 G46 L257 V258 V259 G260 N261 T262 E263 I264 F337 A338 A346 S347 G350 N351 I353 T354 S359 D360 I403 L404	E43 G44 L229 V230 V231 G232 N233 T234 E235 I236 F309 A310 A318 S319 G322 N323 I325 T326 S331 D332 I375 L376
BS06	YSH	A	E802 L873 S876 R880 F914 F1009 T1010 V1011 L1014 P1076 A1079	E769 L840 S843 R847 F881 F976 T977 V978 L981 P1043 A1046	BindingDB: IC50=5.8nM

Gene Ontology

Molecular Function

• GO:0004854 xanthine dehydrogenase activity
• GO:0004855 xanthine oxidase activity
• GO:0005506 iron ion binding
• GO:0016491 oxidoreductase activity
• GO:0030151 molybdenum ion binding
• GO:0042803 protein homodimerization activity
• GO:0043546 molybdopterin cofactor binding
• GO:0046872 metal ion binding
• GO:0050660 flavin adenine dinucleotide binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051537 2 iron, 2 sulfur cluster binding
• GO:0071949 FAD binding

Biological Process

• GO:0009115 xanthine catabolic process

Cellular Component

• GO:0002197 xanthine dehydrogenase complex
• GO:0005576 extracellular region
• GO:0005615 extracellular space
• GO:0005737 cytoplasm
• GO:0005777 peroxisome

External links

• PDB: RCSB:1vdv, PDBe:1vdv, PDBj:1vdv
• PDBsum: 1vdv
• PubMed: 15190124
• UniProt: P80457|XDH_BOVIN Xanthine dehydrogenase/oxidase (Gene Name=XDH)