Structure of PDB 5akk Chain A

Receptor sequence
>5akkA (length=541) Species: 9606 (Homo sapiens) [Search protein sequence]
TLRAAVFDLDGVLALPAVFGVLGRTEEALALPRGLLNDAFQKGGPEGATT
RLMKGEITLSQWIPLMEENCRKCSETAKVCNFSIKEIFDKAISARKINRP
MLQAALMLRKKGFTTAILTNTWLDDRAERDGLAQLMCELKMHFDFLIESC
QVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILVQ
DTDTALKELEKVTGIQLLNTPAPLPTSCNPSDMSHGYVTVKPRVRLHFVE
LGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPPE
IEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVRA
VASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSRT
FKSLFRASDESVLSMHKVAGGLFVNSPEEPSLSRMVTEEEIQFYVQQFKK
SGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQMSQH
MEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDAR
3D structure
PDB5akk Successful Generation of Structural Information for Fragment-Based Drug Discovery.
ChainA
Resolution1.9 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) F267 H334 D335 W336 N359 N378 Y383 Y466 D496 H524
Catalytic site (residue number reindexed from 1) F263 H330 D331 W332 N355 N374 Y379 Y460 D490 H518
Enzyme Commision number 3.1.3.76: lipid-phosphate phosphatase.
3.3.2.10: soluble epoxide hydrolase.
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 1P8 A M310 M339 Y343 N472 A476 M306 M335 Y339 N466 A470 MOAD: ic50=99.3uM
PDBbind-CN: -logKd/Ki=4.00,IC50=99.3uM
BS02 1P8 A P371 M469 N472 P367 M463 N466 MOAD: ic50=99.3uM
PDBbind-CN: -logKd/Ki=4.00,IC50=99.3uM
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004301 epoxide hydrolase activity
GO:0015643 toxic substance binding
GO:0016787 hydrolase activity
GO:0016791 phosphatase activity
GO:0033885 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity
GO:0042577 lipid phosphatase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0052642 lysophosphatidic acid phosphatase activity
Biological Process
GO:0006629 lipid metabolic process
GO:0009056 catabolic process
GO:0009636 response to toxic substance
GO:0010628 positive regulation of gene expression
GO:0016311 dephosphorylation
GO:0042632 cholesterol homeostasis
GO:0046272 stilbene catabolic process
GO:0046839 phospholipid dephosphorylation
GO:0090181 regulation of cholesterol metabolic process
GO:0097176 epoxide metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005777 peroxisome
GO:0005782 peroxisomal matrix
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5akk, PDBe:5akk, PDBj:5akk
PDBsum5akk
PubMed25931264
UniProtP34913|HYES_HUMAN Bifunctional epoxide hydrolase 2 (Gene Name=EPHX2)

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