6ME7

XFEL crystal structure of human melatonin receptor MT2 (H208A) in complex with 2-phenylmelatonin

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	G protein-coupled receptor-like	8091142	3000473	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Rubredoxin-like	8039183	3001257	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	G protein-coupled receptor-like	8091142	3000473	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cytochromes	8057879	3001526	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	G protein-coupled receptor-like	8091142	3000473	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cytochromes	8057879	3001526	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	G protein-coupled receptor-like	8091142	3000473	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	7tm_1_3	e6me7A1	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: 7tm_1_3	ECOD (1.6)
A	Cytochrom_B562_1	e6me7A2	A: alpha bundles	X: Four-helical up-and-down bundle	H: Cytochromes (From Topology)	T: Cytochromes	F: Cytochrom_B562_1	ECOD (1.6)
B	7tm_1_3	e6me7B2	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: 7tm_1_3	ECOD (1.6)
B	Cytochrom_B562_1	e6me7B1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Cytochromes (From Topology)	T: Cytochromes	F: Cytochrom_B562_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.10	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Cytochrome c/b562	CATH (utative)
B	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF07361	Cytochrome b562 (Cytochrom_B562)	Cytochrome b562	-	Family
A, B	PF00001	7 transmembrane receptor (rhodopsin family) (7tm_1)	7 transmembrane receptor (rhodopsin family)	This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GC ...	This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins [1].	Domain
A, B	PF00301	Rubredoxin (Rubredoxin)	Rubredoxin		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin	molecular transducer activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity melatonin receptor activity binding organic cyclic compound binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding molecular transducer activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity melatonin receptor activity binding organic cyclic compound binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	multicellular organismal process regulation of action potential regulation of biological process system process regulation of cellular process nervous system process regulation of system process biological regulation action potential transmission of nerve impulse cell communication regulation of nervous system process neuronal action potential regulation of transmission of nerve impulse regulation of cell communication multicellular organismal process regulation of action potential regulation of biological process system process regulation of cellular process nervous system process regulation of system process biological regulation action potential transmission of nerve impulse cell communication regulation of nervous system process neuronal action potential regulation of transmission of nerve impulse regulation of cell communication cellular process regulation of multicellular organismal process regulation of biological quality regulation of neuronal action potential regulation of membrane potential protein localization regulation of localization establishment of protein localization nitrogen compound transport localization cellular macromolecule localization regulation of peptide hormone secretion regulation of hormone levels establishment of protein localization to extracellular region protein secretion establishment of localization regulation of protein secretion regulation of secretion cellular localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport signaling hormone secretion protein localization to extracellular region peptide secretion secretion by cell regulation of secretion by cell amide transport signal release regulation of signaling secretion regulation of transport regulation of peptide transport regulation of establishment of protein localization cell-cell signaling export from cell regulation of protein transport peptide transport protein transport regulation of cellular localization regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport insulin secretion positive regulation of cell communication positive regulation of biological process positive regulation of transmission of nerve impulse positive regulation of nervous system process positive regulation of multicellular organismal process positive regulation of cellular process negative regulation of nervous system process negative regulation of biological process negative regulation of transmission of nerve impulse negative regulation of cell communication negative regulation of cellular process negative regulation of multicellular organismal process regulation of tube diameter regulation of tube size negative regulation of vasoconstriction circulatory system process regulation of blood circulation vascular process in circulatory system regulation of vasoconstriction blood vessel diameter maintenance vasoconstriction blood circulation regulation of anatomical structure size developmental process sensory organ development eye development animal organ development visual system development multicellular organism development camera-type eye development anatomical structure development sensory system development system development trans-synaptic signaling synaptic signaling anterograde trans-synaptic signaling chemical synaptic transmission negative regulation of cytosolic calcium ion concentration cellular response to stimulus response to stimulus negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of cGMP-mediated signaling negative regulation of cGMP-mediated signaling negative regulation of response to stimulus cGMP-mediated signaling negative regulation of signal transduction regulation of response to stimulus regulation of circadian sleep/wake cycle regulation of circadian sleep/wake cycle, non-REM sleep regulation of circadian rhythm regulation of behavior circadian sleep/wake cycle, non-REM sleep sleep rhythmic process circadian sleep/wake cycle, sleep circadian sleep/wake cycle rhythmic behavior positive regulation of circadian sleep/wake cycle, non-REM sleep circadian rhythm behavior circadian behavior positive regulation of behavior positive regulation of circadian rhythm positive regulation of circadian sleep/wake cycle, sleep regulation of circadian sleep/wake cycle, sleep circadian sleep/wake cycle process G protein-coupled receptor signaling pathway neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death regulation of neuron apoptotic process chemical homeostasis homeostatic process glucose homeostasis carbohydrate homeostasis negative regulation of protein transport negative regulation of transport negative regulation of secretion negative regulation of hormone secretion negative regulation of secretion by cell negative regulation of peptide hormone secretion negative regulation of establishment of protein localization negative regulation of protein secretion negative regulation of peptide secretion negative regulation of protein localization negative regulation of insulin secretion G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger electron transport chain metabolic process generation of precursor metabolites and energy alkane metabolic process catabolic process hydrocarbon catabolic process alkane catabolic process hydrocarbon metabolic process	cellular anatomical structure synapse cell junction cell periphery plasma membrane membrane periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A, B	IPR002278	Melatonin receptor 1A/1B	Family
A, B	IPR000025	Melatonin receptor family	Family
A, B	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
A, B	IPR010980	Cytochrome c/b562	Homologous Superfamily
A, B	IPR009155	Cytochrome b562	Family
A, B	IPR050526	Rubredoxin electron transfer	Family
A, B	IPR018527	Rubredoxin, iron-binding site	Binding Site
A, B	IPR024922	Rubredoxin	Family
A, B	IPR024934	Rubredoxin-like domain	Domain
A, B	IPR024935	Rubredoxin domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P49286	polycystic ovary syndrome type 2 diabetes mellitus gestational diabetes autism spectrum disorder Diabetes Mellitus, Non-Insulin-Dependent maturity-onset diabetes of the young schizophrenia metabolic syndrome X psoriasis conduct disorder major depressive disorder retinal detachment

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Transmembrane	Alpha-helical polytopic	Rhodopsin-like receptors and pumps	G-protein coupled receptors, family A

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	G Protein-Coupled Receptors: Class A	MT₂ melatonin receptor with bound 2-phenylmelatonin

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.