Structure of PDB 1vdv Chain B

Receptor sequence

>1vdvB (length=1296) Species: 9913 (Bos taurus)

ADELVFFVNGKKVVEKNADPETTLLAYLRRKLGLRGTKLGCGEGGCGACT
VMLSKYDRLQDKIIHFSANACLAPICTLHHVAVTTVEGIGSTKTRLHPVQ
ERIAKSHGSQCGFCTPGIVMSMYTLLRNQPEPTVEEIEDAFQGNLCRCTG
YRPILQGFRTFAKSPSLFNPEEFMPLDPTQEPIFPPELLRLKDVPPKQLR
FEGERVTWIQASTLKELLDLKAQHPEAKLVVGNTEIGIEMKFKNQLFPMI
ICPAWIPELNAVEHGPEGISFGAACALSSVEKTLLEAVAKLPTQKTEVFR
GVLEQLRWFAGKQVKSVASLGGNIITASPISDLNPVFMASGTKLTIVSRG
TRRTVPMDHTFFPSYRKTLLGPEEILLSIEIPYSREDEFFSAFKQASRRE
DDIAKVTCGMRVLFQPGSMQVKELALCYGGMADRTISALKTTQKQLSKFW
NEKLLQDVCAGLAEELSLSPDAPGGMIEFRRTLTLSFFFKFYLTVLKKLG
KLDPTYTSATLLFQKHPPANIQLFQEVPNGQSKEDTVGRPLPHLAAAMQA
SGEAVYCDDIPRYENELFLRLVTSTRAHAKIKSIDVSEAQKVPGFVCFLS
ADDIPGSNETGLFNDETVFAKDTVTCVGHIIGAVVADTPEHAERAAHVVK
VTYEDLPAIITIEDAIKNNSFYGSELKIEKGDLKKGFSEADNVVSGELYI
GGQDHFYLETHCTIAIPKGEEGEMELFVSTQNAMKTQSFVAKMLGVPVNR
ILVRVKRMGGGFGGKETRSTLVSVAVALAAYKTGHPVRCMLDRNEDMLIT
GGRHPFLARYKVGFMKTGTIVALEVDHYSNAGNSRDLSHSIMERALFHMD
NCYKIPNIRGTGRLCKTNLSSNTAFRGFGGPQALFIAENWMSEVAVTCGL
PAEEVRWKNMYKEGDLTHFNQRLEGFSVPRCWDECLKSSQYYARKSEVDK
FNKENCWKKRGLCIIPTKFGISFTVPFLNQAGALIHVYTDGSVLVSHGGT
EMGQGLHTKMVQVASKALKIPISKIYISETSTNTVPNSSPTAASVSTDIY
GQAVYEACQTILKRLEPFKKKNPDGSWEDWVMAAYQDRVSLSTTGFYRTP
NLGYSFETNSGNAFHYFTYGVACSEVEIDCLTGDHKNLRTDIVMDVGSSL
NPAIDIGQVEGAFVQGLGLFTLEELHYSPEGSLHTRGPSTYKIPAFGSIP
TEFRVSLLRDCPNKKAIYASKAVGEPPLFLGASVFFAIKDAIRAARAQHT
NNNTKELFRLDSPATPEKIRNACVDKFTTLCVTGAPGNCKPWSLRV

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: B
• 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): Q731 E766 R844 H848 R876 G1224 E1225
• 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	B	A867 S870 R871 S874 S907 N908	A831 S834 R835 S838 S871 N872
BS02	CA	B	H741 Y743 T836 G837	H705 Y707 T800 G801
BS03	FES	B	Q112 C113 G114 C116 C148 C150 L744	Q110 C111 G112 C114 C146 C148 L708
BS04	FES	B	G42 C43 G44 G46 C48 G49 C51 N71 C73	G40 C41 G42 G44 C46 G47 C49 N69 C71
BS05	FAD	B	E45 G46 K256 L257 V258 V259 G260 N261 T262 E263 I264 F337 A338 S347 G350 N351 I353 T354 S359 D360 I403 L404	E43 G44 K228 L229 V230 V231 G232 N233 T234 E235 I236 F309 A310 S319 G322 N323 I325 T326 S331 D332 I375 L376
BS06	YSH	B	E802 L873 S876 R880 F914 F1009 T1010 V1011 L1014 P1076 A1079	E766 L837 S840 R844 F878 F973 T974 V975 L978 P1040 A1043	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)