Structure of PDB 8gc3 Chain D Binding Site BS01

Receptor Information
>8gc3 Chain D (length=742) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HVLRFGGIFEYVESGPMGAEELAFRFAVNTINRNRTLLPNTTLTYDTQKI
NLYDSFEASKKACDQLSLGVAAIFGPSHSSSANAVQSICNALGVPHIQTR
WKHQVSDNKDSFYVSLYPDFSSLSRAILDLVQFFKWKTVTVVYDDSTGLI
RLQELIKAPSRYNLRLKIRQLPADTKDAKPLLKEMKRGKEFHVIFDCSHE
MAAGILKQALAMGMMTEYYHYIFTTLDLFALDVEPYRYSGVNMTGFRILN
TENTQVSSIIEKWSMERLQAPPKPDSGLLDGFMTTDAALMYDAVHVVSVA
VQQFPQMTVSSLQCNRHKPWRFGTRFMSLIKEAHWEGLTGRITFNKTNGL
RTDFDLDVISLKEEGLEKIGTWDPASGLNMTESQKGKPANITDSLSNRSL
IVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLV
EDGKYGAQDDVNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPF
MTLGISILYRKPNGTNPGVFSFLNPLSPDIWMYVLLAYLGVSVVLFVILS
TRIVGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQTKIEY
GAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSD
YAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAI
LQLQEEGKLHMMKEKWWRGVQNIGGIFIVLAAGLVLSVFVAV
Ligand information
Ligand IDMAN
InChIInChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5+,6+/m1/s1
InChIKeyWQZGKKKJIJFFOK-PQMKYFCFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C1C(C(C(C(O1)O)O)O)O)O
CACTVS 3.341OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O)O)O)O)O
ACDLabs 10.04OC1C(O)C(OC(O)C1O)CO
FormulaC6 H12 O6
Namealpha-D-mannopyranose;
alpha-D-mannose;
D-mannose;
mannose
ChEMBLCHEMBL365590
DrugBank
ZINCZINC000003860903
PDB chain8gc3 Chain L Residue 4 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8gc3 Structural basis for kainate receptor activation by a partial agonist
Resolution3.8 Å
Binding residue
(original residue number in PDB)		R158 D162
Binding residue
(residue number reindexed from 1)		R125 D129
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000149 SNARE binding
GO:0004970 glutamate-gated receptor activity
GO:0005216 monoatomic ion channel activity
GO:0005234 extracellularly glutamate-gated ion channel activity
GO:0005515 protein binding
GO:0008066 glutamate receptor activity
GO:0015276 ligand-gated monoatomic ion channel activity
GO:0015277 kainate selective glutamate receptor activity
GO:0022849 glutamate-gated calcium ion channel activity
GO:0030165 PDZ domain binding
GO:0031624 ubiquitin conjugating enzyme binding
GO:0031625 ubiquitin protein ligase binding
GO:0038023 signaling receptor activity
GO:0042802 identical protein binding
GO:0097110 scaffold protein binding
GO:0099507 ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential
GO:1904315 transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential
Biological Process
GO:0001662 behavioral fear response
GO:0006811 monoatomic ion transport
GO:0006874 intracellular calcium ion homeostasis
GO:0007268 chemical synaptic transmission
GO:0019228 neuronal action potential
GO:0019722 calcium-mediated signaling
GO:0034220 monoatomic ion transmembrane transport
GO:0035235 ionotropic glutamate receptor signaling pathway
GO:0035249 synaptic transmission, glutamatergic
GO:0042391 regulation of membrane potential
GO:0043113 receptor clustering
GO:0043524 negative regulation of neuron apoptotic process
GO:0043525 positive regulation of neuron apoptotic process
GO:0046328 regulation of JNK cascade
GO:0048169 regulation of long-term neuronal synaptic plasticity
GO:0048172 regulation of short-term neuronal synaptic plasticity
GO:0050804 modulation of chemical synaptic transmission
GO:0050806 positive regulation of synaptic transmission
GO:0051402 neuron apoptotic process
GO:0051967 negative regulation of synaptic transmission, glutamatergic
GO:0060079 excitatory postsynaptic potential
GO:0060080 inhibitory postsynaptic potential
GO:0098815 modulation of excitatory postsynaptic potential
GO:0099171 presynaptic modulation of chemical synaptic transmission
GO:0099505 regulation of presynaptic membrane potential
GO:0120169 detection of cold stimulus involved in thermoception
Cellular Component
GO:0005886 plasma membrane
GO:0008328 ionotropic glutamate receptor complex
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0030424 axon
GO:0030425 dendrite
GO:0032839 dendrite cytoplasm
GO:0032983 kainate selective glutamate receptor complex
GO:0042734 presynaptic membrane
GO:0043025 neuronal cell body
GO:0043195 terminal bouton
GO:0043204 perikaryon
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0097471 mossy fiber rosette
GO:0098686 hippocampal mossy fiber to CA3 synapse
GO:0098839 postsynaptic density membrane
GO:0098978 glutamatergic synapse

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8gc3, PDBe:8gc3, PDBj:8gc3
PDBsum8gc3
PubMed
UniProtP42260|GRIK2_RAT Glutamate receptor ionotropic, kainate 2 (Gene Name=Grik2)

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