Structure of PDB 4pe5 Chain C Binding Site BS02

Receptor Information

>4pe5 Chain C (length=754) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

KIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLQATSVTHKPNAIQM
ALSVCEDLISSQVYAILVSHTPTPVSYTAGFYRIPVLGLTTRMSIYSDKS
IHLSFLRTVPPYSHQSSVWFEMMRVYNWNHIILLVSDDHEGRAAQKRLET
LLEERESKAEKVLQFDPGTKNVTALLMEARELEARVIILSASEDDAATVY
RAAAMLDMTGSGYVWLVGEREISGNALRYAPDGIIGLQLINGKNESAHIS
DAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYAD
GVTGRVEFNEDGDRKFAQYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWP
GGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVK
KVICTGPNDGSPRHTVPQCCYGFCIDLLIKLARTMQFTYEVHLVADGKFG
TQERVQNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKY
QGLTILVKKEIPRFMQPFQSCLWLLVGLSVHVVAVMLYLLDRSAMWFSWG
VLLNMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKF
IYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAF
IWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQQVSLSILKS
HENGFMEDLDKTWVRYQECDSRSNAPATLTCENMAGVFMLVAGGIVAGIF
LIFI

Ligand information

Ligand ID

GLY

InChI

InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)

InChIKey

DHMQDGOQFOQNFH-UHFFFAOYSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	C(C(=O)O)N
CACTVS 3.341	NCC(O)=O
ACDLabs 10.04	O=C(O)CN

Formula

C2 H5 N O2

Name

GLYCINE

PDB chain

4pe5 Chain C Residue 940 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	4pe5 Crystal structure of a heterotetrameric NMDA receptor ion channel.
Resolution	3.96 Å
Binding residue (original residue number in PDB)	F484 P516 L517 T518 R523 S688 W731 D732
Binding residue (residue number reindexed from 1)	F449 P481 L482 T483 R488 S609 W652 D653
Annotation score	1

Enzymatic activity

Enzyme Commision number

Gene Ontology

	Molecular Function
GO:0001540	amyloid-beta binding
GO:0004970	glutamate-gated receptor activity
GO:0004972	NMDA glutamate receptor activity
GO:0005102	signaling receptor binding
GO:0005216	monoatomic ion channel activity
GO:0005261	monoatomic cation channel activity
GO:0005262	calcium channel activity
GO:0005509	calcium ion binding
GO:0005515	protein binding
GO:0005516	calmodulin binding
GO:0015276	ligand-gated monoatomic ion channel activity
GO:0015280	ligand-gated sodium channel activity
GO:0016594	glycine binding
GO:0016595	glutamate binding
GO:0019899	enzyme binding
GO:0019902	phosphatase binding
GO:0022843	voltage-gated monoatomic cation channel activity
GO:0022849	glutamate-gated calcium ion channel activity
GO:0035254	glutamate receptor binding
GO:0038023	signaling receptor activity
GO:0044877	protein-containing complex 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:0001661	conditioned taste aversion
GO:0001666	response to hypoxia
GO:0001964	startle response
GO:0001967	suckling behavior
GO:0001975	response to amphetamine
GO:0006366	transcription by RNA polymerase II
GO:0006811	monoatomic ion transport
GO:0006812	monoatomic cation transport
GO:0006816	calcium ion transport
GO:0006874	intracellular calcium ion homeostasis
GO:0007268	chemical synaptic transmission
GO:0007611	learning or memory
GO:0007612	learning
GO:0007613	memory
GO:0007616	long-term memory
GO:0008306	associative learning
GO:0008344	adult locomotory behavior
GO:0008355	olfactory learning
GO:0008542	visual learning
GO:0010524	positive regulation of calcium ion transport into cytosol
GO:0010646	regulation of cell communication
GO:0014070	response to organic cyclic compound
GO:0014075	response to amine
GO:0018964	propylene metabolic process
GO:0019233	sensory perception of pain
GO:0019722	calcium-mediated signaling
GO:0021586	pons maturation
GO:0021987	cerebral cortex development
GO:0034220	monoatomic ion transmembrane transport
GO:0035176	social behavior
GO:0035235	ionotropic glutamate receptor signaling pathway
GO:0035249	synaptic transmission, glutamatergic
GO:0035725	sodium ion transmembrane transport
GO:0042391	regulation of membrane potential
GO:0043065	positive regulation of apoptotic process
GO:0043278	response to morphine
GO:0043523	regulation of neuron apoptotic process
GO:0043524	negative regulation of neuron apoptotic process
GO:0043576	regulation of respiratory gaseous exchange
GO:0045471	response to ethanol
GO:0045944	positive regulation of transcription by RNA polymerase II
GO:0048167	regulation of synaptic plasticity
GO:0048168	regulation of neuronal synaptic plasticity
GO:0048169	regulation of long-term neuronal synaptic plasticity
GO:0048511	rhythmic process
GO:0048814	regulation of dendrite morphogenesis
GO:0050770	regulation of axonogenesis
GO:0050905	neuromuscular process
GO:0051290	protein heterotetramerization
GO:0051592	response to calcium ion
GO:0051963	regulation of synapse assembly
GO:0051968	positive regulation of synaptic transmission, glutamatergic
GO:0055074	calcium ion homeostasis
GO:0060079	excitatory postsynaptic potential
GO:0060134	prepulse inhibition
GO:0060179	male mating behavior
GO:0060992	response to fungicide
GO:0065003	protein-containing complex assembly
GO:0070050	neuron cellular homeostasis
GO:0070588	calcium ion transmembrane transport
GO:0071287	cellular response to manganese ion
GO:0097553	calcium ion transmembrane import into cytosol
GO:0098655	monoatomic cation transmembrane transport
GO:0099505	regulation of presynaptic membrane potential
GO:1900149	positive regulation of Schwann cell migration
GO:1902952	positive regulation of dendritic spine maintenance
GO:1903428	positive regulation of reactive oxygen species biosynthetic process
GO:1903539	protein localization to postsynaptic membrane
GO:1904062	regulation of monoatomic cation transmembrane transport
GO:1904646	cellular response to amyloid-beta
GO:1905429	response to glycine
GO:1905430	cellular response to glycine
GO:2000463	positive regulation of excitatory postsynaptic potential

	Cellular Component
GO:0005737	cytoplasm
GO:0005783	endoplasmic reticulum
GO:0005789	endoplasmic reticulum membrane
GO:0005886	plasma membrane
GO:0008021	synaptic vesicle
GO:0009986	cell surface
GO:0014069	postsynaptic density
GO:0016020	membrane
GO:0017146	NMDA selective glutamate receptor complex
GO:0030425	dendrite
GO:0030672	synaptic vesicle membrane
GO:0032590	dendrite membrane
GO:0042734	presynaptic membrane
GO:0043005	neuron projection
GO:0043025	neuronal cell body
GO:0043083	synaptic cleft
GO:0043195	terminal bouton
GO:0043197	dendritic spine
GO:0044307	dendritic branch
GO:0045202	synapse
GO:0045211	postsynaptic membrane
GO:0048787	presynaptic active zone membrane
GO:0060076	excitatory synapse
GO:0097060	synaptic membrane
GO:0098686	hippocampal mossy fiber to CA3 synapse
GO:0098688	parallel fiber to Purkinje cell synapse
GO:0098839	postsynaptic density membrane
GO:0098978	glutamatergic synapse

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:4pe5, PDBe:4pe5, PDBj:4pe5
PDBsum	4pe5
PubMed	24876489
UniProt	P35439\|NMDZ1_RAT Glutamate receptor ionotropic, NMDA 1 (Gene Name=Grin1)

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