Structure of PDB 2ymd Chain B

Receptor sequence

>2ymdB (length=210) Species: 6500 (Aplysia californica)

QANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKVDSSTNEVDL
VYWEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYESTRPVQVL
SPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGVTCALTFGSWVYSGF
EIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVV
KFRERRAGNG

3D structure

• PDB: 2ymd Structural Basis of Ligand Recognition in 5-Ht(3) Receptors.
• Chain: B
• Resolution: 1.96 Å

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	SRO	B	I104 V106 M114 I116	I104 V106 M114 I116	MOAD: Kd=693uM PDBbind-CN: -logKd/Ki=3.16,Kd=693uM
BS02	SRO	B	Y91 W145 V146 C188 C189 Y193	Y91 W145 V146 C188 C189 Y193	MOAD: Kd=693uM PDBbind-CN: -logKd/Ki=3.16,Kd=693uM

Gene Ontology

Molecular Function

• GO:0004888 transmembrane signaling receptor activity
• GO:0005216 monoatomic ion channel activity
• GO:0005230 extracellular ligand-gated monoatomic ion channel activity
• GO:0005231 excitatory extracellular ligand-gated monoatomic ion channel activity
• GO:0005515 protein binding
• GO:0042802 identical protein binding
• GO:0046872 metal ion binding
• GO:1904315 transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential

Biological Process

• GO:0006811 monoatomic ion transport
• GO:0007165 signal transduction
• GO:0007268 chemical synaptic transmission
• GO:0034220 monoatomic ion transmembrane transport
• GO:0042391 regulation of membrane potential
• GO:0050877 nervous system process
• GO:0060078 regulation of postsynaptic membrane potential
• GO:0060079 excitatory postsynaptic potential

Cellular Component

• GO:0016020 membrane
• GO:0043005 neuron projection
• GO:0045202 synapse
• GO:0098794 postsynapse

External links

• PDB: RCSB:2ymd, PDBe:2ymd, PDBj:2ymd
• PDBsum: 2ymd
• PubMed: 23196367
• UniProt: Q8WSF8