Structure of PDB 3bdj Chain A

Receptor sequence

>3bdjA (length=1286) Species: 9913 (Bos taurus)

ADELVFFVNGKKVVEKNADPETTLLAYLRRKLGLRGTKLGCGEGGCGACT
VMLSKYDRLQDKIIHFSANACLAPICTLHHVAVTTVEGIGSTKTRLHPVQ
ERIAKSHGSQCGFCTPGIVMSMYTLLRNQPEPTVEEIEDAFQGNLCRCTG
YRPILQGFRTFAPSLFNPEEFMPLDPTQEPIFPPELLRLKDVPPKQLRFE
GERVTWIQASTLKELLDLKAQHPEAKLVVGNTEIGIEMKFKNQLFPMIIC
PAWIPELNAVEHGPEGISFGAACALSSVEKTLLEAVAKLPTQKTEVFRGV
LEQLRWFAGKQVKSVASLGGNIITASPISDLNPVFMASGTKLTIVSRGTR
RTVPMDHTFFPSYRKTLLGPEEILLSIEIPYSREDEFFSAFKQASRREDD
IAKVTCGMRVLFQPGSMQVKELALCYGGMADRTISALKTTQKQLSKFWNE
KLLQDVCAGLAEELSLSPDAPGGMIEFRRTLTLSFFFKFYLTVLKKLGKL
DPTYTSATLLFQKHPPANIQLFQEVPNGQSKEDTVGRPLPHLAAAMQASG
EAVYCDDIPRYENELFLRLVTSTRAHAKIKSIDVSEAQKVPGFVCFLSAD
DIPGSNETGLFNDETVFAKDTVTCVGHIIGAVVADTPEHAERAAHVVKVT
YEDLPAIITIEDAIKNNSFYGSELKIEKGDLKKGFSEADNVVSGELYIGG
QDHFYLETHCTIAIPKGEEGEMELFVSTQNAMKTQSFVAKMLGVPVNRIL
VRVKRMGGGFGGKETRSTLVSVAVALAAYKTGHPVRCMLDRNEDMLITGG
RHPFLARYKVGFMKTGTIVALEVDHYSNAGNSRDLSHSIMERALFHMDNC
YKIPNIRGTGRLCKTNLSSNTAFRGFGGPQALFIAENWMSEVAVTCGLPA
EEVRWKNMYKEGDLTHFNQRLEGFSVPRCWDECLKSSQYYARKSEVDKFN
KENCWKKRGLCIIPTKFGISFTVPFLNQAGALIHVYTDGSVLVSHGGTEM
GQGLHTKMVQVASKALKIPISKIYISETSTNTVPNSSPTAASVSTDIYGQ
AVYEACQTILKRLEPFKKKNPDGSWEDWVMAAYQDRVSLSTTGFYRTPNL
GYSFETNSGNAFHYFTYGVACSEVEIDCLTGDHKNLRTDIVMDVGSSLNP
AIDIGQVEGAFVQGLGLFTLEELHYSPEGSLHTRGPSTYKIPAFGSIPTE
FRVSLLRDCPNKKAIYASKAVGEPPLFLGASVFFAIKDAIRAARAQHTNN
NTKELFRLDSPATPEKIRNACVDKFTTLCKPWSLRV

3D structure

• PDB: 3bdj Mechanism of inhibition of xanthine oxidoreductase by allopurinol: crystal structure of reduced bovine milk xanthine oxidoreductase bound with oxipurinol.
• Chain: A
• Resolution: 2.0 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Q767 E802 R880 H884 R912 G1260 E1261
• Catalytic site (residue number reindexed from 1): Q729 E764 R842 H846 R874 G1222 E1223
• 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	A829 S832 R833 S836 S869 N870
BS02	FES	A	Q112 C113 G114 C116 C148 C150 L744	Q110 C111 G112 C114 C146 C148 L706
BS03	FES	A	G42 C43 G44 G46 C48 G49 C51 N71 C73	G40 C41 G42 G44 C46 G47 C49 N69 C71
BS04	MOW	A	G799 A910 F911 R912 E1261	G761 A872 F873 R874 E1223
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 L227 V228 V229 G230 N231 T232 E233 I234 F307 A308 A316 S317 G320 N321 I323 T324 S329 D330 I373 L374
BS06	141	A	E802 R880 F914 F1009 T1010 A1078 A1079 E1261	E764 R842 F876 F971 T972 A1040 A1041 E1223
BS07	CO3	A	R839 H840 T909 A910 F914 G915 Q918	R801 H802 T871 A872 F876 G877 Q880

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:3bdj, PDBe:3bdj, PDBj:3bdj
• PDBsum: 3bdj
• PubMed: 18600558
• UniProt: P80457|XDH_BOVIN Xanthine dehydrogenase/oxidase (Gene Name=XDH)