Structure of PDB 2ckj Chain B

Receptor sequence

>2ckjB (length=1289) Species: 9606 (Homo sapiens)

TADKLVFFVNGRKVVEKNADPETTLLAYLRRKLGLSGTKLGCGEGGCGAC
TVMLSKYDRLQNKIVHFSANACLAPICSLHHVAVTTVEGIGSTKTRLHPV
QERIAKSHGSQCGFCTPGIVMSMYTLLRNQPEPTMEEIENAFQGNLCRCT
GYRPILQGFRTFARPSLFKPEEFTPLDPTQEPIFPPELLRLKDTPRKQLR
FEGERVTWIQASTLKELLDLKAQHPDAKLVVGNTEIGIEMKFKNMLFPMI
VCPAWIPELNSVEHGPDGISFGAACPLSIVEKTLVDAVAKLPAQKTEVFR
GVLEQLRWFAGKQVKSVASVGGNIITASPISDLNPVFMASGAKLTLVSRG
TRRTVQMDHTFFPGYRKTLLSPEEILLSIEIPYSREGEYFSAFKQASRRE
DDIAKVTSGMRVLFKPGTTEVQELALCYGGMANRTISALKTTQRQLSKLW
KEELLQDVCAGLAEELHLPPDAPGGMVDFRCTLTLSFFFKFYLTVLQKLG
QENLEDKCGKLDPTFASATDVQLFQEVPKGQSEEDMVGRPLPHLAADMQA
SGEAVYCDDIPRYENELSLRLVTSTRAHAKIKSIDTSEAKKVPGFVCFIS
ADDVPGSNITGICNDETVFAKDKVTCVGHIIGAVVADTPEHTQRAAQGVK
ITYEELPAIITIEDAIKNNSFYGPELKIEKGDLKKGFSEADNVVSGEIYI
GGQEHFYLETHCTIAVPKGEAGEMELFVSTQNTMKTQSFVAKMLGVPANR
IVVRVKRMGGGFGGKETRSTVVSTAVALAAYKTGRPVRCMLDRDEDMLIT
GGRHPFLARYKVGFMKTGTVVALEVDHFSNVGNTQDLSQSIMERALFHMD
NCYKIPNIRGTGRLCKTNLPSNTAFRGFGGPQGMLIAECWMSEVAVTCGM
PAEEVRRKNLYKEGDLTHFNQKLEGFTLPRCWEECLASSQYHARKSEVDK
FNKENCWKKRGLCIIPTKFGISFTVPFLNQAGALLHVYTDGSVLLTHGGT
EMGQGLHTKMVQVASRALKIPTSKIYISETSTNTVPNTSPTAASVSADLN
GQAVYAACQTILKRLEPYKKKNPSGSWEDWVTAAYMDTVSLSATGFYRTP
NLGYSFETNSGNPFHYFSYGVACSEVEIDCLTGDHKNLRTDIVMDVGSSL
NPAIDIGQVEGAFVQGLGLFTLEELHYSPEGSLHTRGPSTYKIPAFGSIP
IEFRVSLLRDCPNKKAIYASKAVGEPPLFLAASIFFAIKDAIRAARAQHT
GNNVKELFRLDSPATPEKIRNACVDKFTTLCVCKPWSVR

3D structure

• PDB: 2ckj Human Milk Xanthine Dehydrogenase is Incompletely Converted to the Oxidase Form in the Absence of Proteolysis. A Structural Explanation.
• Chain: B
• Resolution: 3.59 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Q768 E803 R881 H885 R913 G1261 E1262
• 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	FES	B	Q112 C113 G114 C116 C148 C150	Q111 C112 G113 C115 C147 C149
BS02	FES	B	G42 C43 G44 G46 C48 G49 C51 C73	G41 C42 G43 G45 C47 G48 C50 C72
BS03	FAD	B	L257 V259 G260 N261 T262 E263 I264 F337 A338 A346 S347 G350 N351 I353 S359 D360 L404	L229 V231 G232 N233 T234 E235 I236 F309 A310 A318 S319 G322 N323 I325 S331 D332 L376

Gene Ontology

Molecular Function

• GO:0004854 xanthine dehydrogenase activity
• GO:0004855 xanthine oxidase activity
• GO:0005506 iron ion binding
• GO:0005515 protein binding
• GO:0016491 oxidoreductase activity
• 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:0070674 hypoxanthine dehydrogenase activity
• GO:0070675 hypoxanthine oxidase activity
• GO:0071949 FAD binding

Biological Process

• GO:0000255 allantoin metabolic process
• GO:0001933 negative regulation of protein phosphorylation
• GO:0001937 negative regulation of endothelial cell proliferation
• GO:0006147 guanine catabolic process
• GO:0006148 inosine catabolic process
• GO:0006149 deoxyinosine catabolic process
• GO:0006154 adenosine catabolic process
• GO:0006157 deoxyadenosine catabolic process
• GO:0006161 deoxyguanosine catabolic process
• GO:0006196 AMP catabolic process
• GO:0006204 IMP catabolic process
• GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process
• GO:0007595 lactation
• GO:0009114 hypoxanthine catabolic process
• GO:0009115 xanthine catabolic process
• GO:0010629 negative regulation of gene expression
• GO:0016226 iron-sulfur cluster assembly
• GO:0030856 regulation of epithelial cell differentiation
• GO:0043605 amide catabolic process
• GO:0045602 negative regulation of endothelial cell differentiation
• GO:0046038 GMP catabolic process
• GO:0046055 dGMP catabolic process
• GO:0046059 dAMP catabolic process
• GO:0051898 negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
• GO:1900745 positive regulation of p38MAPK cascade
• GO:1900747 negative regulation of vascular endothelial growth factor signaling pathway
• GO:2000379 positive regulation of reactive oxygen species metabolic process
• GO:2001213 negative regulation of vasculogenesis

Cellular Component

• GO:0005576 extracellular region
• GO:0005615 extracellular space
• GO:0005737 cytoplasm
• GO:0005777 peroxisome
• GO:0005829 cytosol
• GO:0016529 sarcoplasmic reticulum

External links

• PDB: RCSB:2ckj, PDBe:2ckj, PDBj:2ckj
• PDBsum: 2ckj
• UniProt: P47989|XDH_HUMAN Xanthine dehydrogenase/oxidase (Gene Name=XDH)