Structure of PDB 2dy5 Chain A

Receptor sequence
>2dy5A (length=214) Species: 10116 (Rattus norvegicus) [Search protein sequence]
SQDLSEALKEATKEVHIRAENSEFMRNFQKGQVSREGFKLVMASLYHIYT
ALEEEIERNKQNPVYAPLYFPEELHRRAALEQDMAFWYGPHWQEAIPYTP
ATQHYVKRLHEVGGTHPELLVAHAYTRYLGDLSGGQVLKKIAQKAMALPS
SGEGLAFFTFPSIDNPTKFKQLYRARMNTLEMTPEVKHRVTEEAKTAFLL
NIELFEELQALLTE
3D structure
PDB2dy5 X-ray crystallographic and biochemical characterization of the inhibitory action of an imidazole-dioxolane compound on heme oxygenase
ChainA
Resolution2.7 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) N30 Y58 T135 R136 G139 D140 G144
Catalytic site (residue number reindexed from 1) N21 Y49 T126 R127 G130 D131 G135
Enzyme Commision number 1.14.14.18: heme oxygenase (biliverdin-producing).
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 HEM A H25 E29 M34 Y134 G139 S142 L147 K179 F207 N210 H16 E20 M25 Y125 G130 S133 L138 K170 F198 N201
BS02 224 A F37 V50 G139 D140 G143 L147 F167 F28 V41 G130 D131 G134 L138 F158 BindingDB: IC50=2800nM
Gene Ontology
Molecular Function
GO:0004392 heme oxygenase (decyclizing) activity
GO:0004630 phospholipase D activity
GO:0005198 structural molecule activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0019899 enzyme binding
GO:0020037 heme binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0052869 arachidonate omega-hydroxylase activity
Biological Process
GO:0001525 angiogenesis
GO:0001666 response to hypoxia
GO:0002246 wound healing involved in inflammatory response
GO:0006357 regulation of transcription by RNA polymerase II
GO:0006644 phospholipid metabolic process
GO:0006788 heme oxidation
GO:0006879 intracellular iron ion homeostasis
GO:0006915 apoptotic process
GO:0006979 response to oxidative stress
GO:0007264 small GTPase-mediated signal transduction
GO:0008217 regulation of blood pressure
GO:0008285 negative regulation of cell population proliferation
GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage
GO:0009410 response to xenobiotic stimulus
GO:0010656 negative regulation of muscle cell apoptotic process
GO:0016236 macroautophagy
GO:0016239 positive regulation of macroautophagy
GO:0016242 negative regulation of macroautophagy
GO:0031670 cellular response to nutrient
GO:0032764 negative regulation of mast cell cytokine production
GO:0034101 erythrocyte homeostasis
GO:0034605 cellular response to heat
GO:0035094 response to nicotine
GO:0035556 intracellular signal transduction
GO:0042167 heme catabolic process
GO:0042168 heme metabolic process
GO:0042542 response to hydrogen peroxide
GO:0043305 negative regulation of mast cell degranulation
GO:0043524 negative regulation of neuron apoptotic process
GO:0043627 response to estrogen
GO:0045766 positive regulation of angiogenesis
GO:0048661 positive regulation of smooth muscle cell proliferation
GO:0048662 negative regulation of smooth muscle cell proliferation
GO:0060586 multicellular organismal-level iron ion homeostasis
GO:0071243 cellular response to arsenic-containing substance
GO:0071276 cellular response to cadmium ion
GO:0072719 cellular response to cisplatin
GO:0090050 positive regulation of cell migration involved in sprouting angiogenesis
GO:0097421 liver regeneration
GO:0110076 negative regulation of ferroptosis
GO:1902042 negative regulation of extrinsic apoptotic signaling pathway via death domain receptors
GO:1903589 positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis
GO:1904019 epithelial cell apoptotic process
GO:1904036 negative regulation of epithelial cell apoptotic process
GO:1904037 positive regulation of epithelial cell apoptotic process
GO:1904550 response to arachidonate
GO:1904681 response to 3-methylcholanthrene
GO:1904706 negative regulation of vascular associated smooth muscle cell proliferation
Cellular Component
GO:0005634 nucleus
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0005901 caveola
GO:0016020 membrane
GO:0048471 perinuclear region of cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2dy5, PDBe:2dy5, PDBj:2dy5
PDBsum2dy5
PubMed17253780
UniProtP06762|HMOX1_RAT Heme oxygenase 1 (Gene Name=Hmox1)

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