5SVM | pdb_00005svm

Crystal structure of the ATP-gated human P2X3 ion channel bound to agonist 2-methylthio-ATP in the desensitized state

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
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	P2X receptor-like	8053195	3002165	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	P2X receptor-like	8053195	3002165	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		e5svmA1	A: cradle loop barrel	X: RIFT-related	H: Alanine racemase-C	T: GTP_EFTU_D2	F:	ECOD (20:10:01)
B		e5svmB1	A: cradle loop barrel	X: RIFT-related	H: Alanine racemase-C	T: GTP_EFTU_D2	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.287.940	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	atp-gated p2x4 ion channel	CATH (4.3.0)
A	2.60.490.10	Mainly Beta	Sandwich	atp-gated p2x4 ion channel fold	atp-gated p2x4 ion channel domain	CATH (4.3.0)
B	1.10.287.940	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	atp-gated p2x4 ion channel	CATH (4.3.0)
B	2.60.490.10	Mainly Beta	Sandwich	atp-gated p2x4 ion channel fold	atp-gated p2x4 ion channel domain	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	P2X purinoceptor 3	monoatomic cation transmembrane transporter activity extracellularly ATP-gated monoatomic cation channel activity gated channel activity monoatomic ion channel activity ATP-gated ion channel activity excitatory extracellular ligand-gated monoatomic ion channel activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity monoatomic cation channel activity passive transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transporter activity ligand-gated monoatomic cation channel activity monoatomic cation transmembrane transporter activity extracellularly ATP-gated monoatomic cation channel activity gated channel activity monoatomic ion channel activity ATP-gated ion channel activity excitatory extracellular ligand-gated monoatomic ion channel activity ligand-gated channel activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity monoatomic cation channel activity passive transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transporter activity ligand-gated monoatomic cation channel activity transmembrane transporter activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity purinergic nucleotide receptor activity nucleotide receptor activity cation binding metal ion binding	multicellular organismal process system process smooth muscle contraction phasic smooth muscle contraction muscle contraction peristalsis muscle system process cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process multicellular organismal process system process smooth muscle contraction phasic smooth muscle contraction muscle contraction peristalsis muscle system process cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of calcium-mediated signaling positive regulation of calcium-mediated signaling signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction regulation of response to stimulus calcium-mediated signaling regulation of cell communication cellular process positive regulation of signaling response to stress response to abiotic stimulus response to cold response to temperature stimulus sensory perception of chemical stimulus sensory perception nervous system process sensory perception of taste trans-synaptic signaling cell-cell signaling chemical synaptic transmission synaptic signaling anterograde trans-synaptic signaling neuromuscular synaptic transmission behavior multicellular organismal response to stress response to pain behavioral response to pain localization cellular localization establishment of localization in cell establishment of localization transport monoatomic ion transmembrane transport calcium ion transport metal ion transport monoatomic cation transmembrane transport transmembrane transport monoatomic ion transport monoatomic cation transport calcium ion transmembrane transport response to mechanical stimulus response to external stimulus urinary bladder smooth muscle contraction urinary tract smooth muscle contraction regulation of localization regulation of calcium ion transport positive regulation of cation transmembrane transport positive regulation of calcium ion transport regulation of calcium ion transport into cytosol regulation of monoatomic ion transmembrane transport regulation of calcium ion transmembrane transport positive regulation of monoatomic ion transport positive regulation of calcium ion transmembrane transport positive regulation of transmembrane transport positive regulation of monoatomic ion transmembrane transport regulation of biological quality regulation of metal ion transport calcium ion transmembrane import into cytosol regulation of transport regulation of monoatomic ion transport positive regulation of cytosolic calcium ion concentration positive regulation of calcium ion transport into cytosol regulation of transmembrane transport positive regulation of transport regulation of cellular localization regulation of monoatomic cation transmembrane transport calcium ion transport into cytosol regulation of synaptic plasticity modulation of chemical synaptic transmission regulation of trans-synaptic signaling response to decreased oxygen levels response to hypoxia response to oxygen levels cellular response to nitrogen compound cellular response to ATP response to organophosphorus response to oxygen-containing compound response to nitrogen compound response to ATP response to purine-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical protein-containing complex organization protein trimerization cellular component organization cellular component biogenesis cellular component assembly protein homotrimerization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis response to heat response to carbohydrate	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex receptor complex neuron to neuron synapse synapse cell junction hippocampal mossy fiber to CA3 synapse Schaffer collateral - CA1 synapse axon cell projection neuron projection cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex receptor complex neuron to neuron synapse synapse cell junction hippocampal mossy fiber to CA3 synapse Schaffer collateral - CA1 synapse axon cell projection neuron projection plasma membrane bounded cell projection postsynapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR059116	ATP P2X receptor-like	Family
A, B	IPR053792	ATP P2X receptor, conserved site	Conserved Site
A, B	IPR003046	P2X3 purinoceptor	Family
A, B	IPR001429	P2X purinoreceptor	Family
A, B	IPR027309	P2X purinoreceptor extracellular domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P56373	Hyperalgesia Crohn disease Hodgkins lymphoma nervous system injury

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Transmembrane	Alpha-helical polytopic	ENaC/P2X	ATP-gated cation channel

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Other Ion Channels	ATP-gated P2X₃ ion channel, closed apo state

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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