Structure of PDB 4pam Chain A Binding Site BS01

Receptor Information

>4pam Chain A (length=337) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

DKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHE
AGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDAARADDARQLF
VLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLND
LDRIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGIHCFEG
VTAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILF
LNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTK
EIYTHFTCATDTKNVQFVCDAVTDVIIKNNLKDCGLF

Ligand information

Ligand ID

GDP

InChI

InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1

InChIKey

QGWNDRXFNXRZMB-UUOKFMHZSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.6	c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385	NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385	NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01	O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6	c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N

Formula

C10 H15 N5 O11 P2

Name

GUANOSINE-5'-DIPHOSPHATE

PDB chain

4pam Chain A Residue 401 [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	4pam A Conserved Phenylalanine as a Relay between the alpha 5 Helix and the GDP Binding Region of Heterotrimeric Gi Protein alpha Subunit.
Resolution	2.101 Å
Binding residue (original residue number in PDB)	E43 G45 K46 S47 T48 L175 R176 T177 N269 K270 D272 L273 C325 A326 T327
Binding residue (residue number reindexed from 1)	E35 G37 K38 S39 T40 L167 R168 T169 N252 K253 D255 L256 C308 A309 T310
Annotation score	4

Enzymatic activity

Catalytic site (original residue number in PDB)	E43 T48 R178 D200
Catalytic site (residue number reindexed from 1)	E35 T40 R170 D192
Enzyme Commision number	?

Gene Ontology

	Molecular Function
GO:0000287	magnesium ion binding
GO:0001664	G protein-coupled receptor binding
GO:0003924	GTPase activity
GO:0005515	protein binding
GO:0005525	GTP binding
GO:0016787	hydrolase activity
GO:0019001	guanyl nucleotide binding
GO:0019003	GDP binding
GO:0031683	G-protein beta/gamma-subunit complex binding
GO:0031749	D2 dopamine receptor binding
GO:0031821	G protein-coupled serotonin receptor binding
GO:0032794	GTPase activating protein binding
GO:0046872	metal ion binding

	Biological Process
GO:0007165	signal transduction
GO:0007186	G protein-coupled receptor signaling pathway
GO:0007188	adenylate cyclase-modulating G protein-coupled receptor signaling pathway
GO:0043949	regulation of cAMP-mediated signaling
GO:0050805	negative regulation of synaptic transmission
GO:0051301	cell division
GO:0060236	regulation of mitotic spindle organization
GO:0099645	neurotransmitter receptor localization to postsynaptic specialization membrane
GO:1904322	cellular response to forskolin
GO:1904778	positive regulation of protein localization to cell cortex

	Cellular Component
GO:0005634	nucleus
GO:0005737	cytoplasm
GO:0005813	centrosome
GO:0005834	heterotrimeric G-protein complex
GO:0005856	cytoskeleton
GO:0005886	plasma membrane
GO:0005938	cell cortex
GO:0030496	midbody
GO:0032991	protein-containing complex
GO:0098794	postsynapse
GO:0098978	glutamatergic synapse

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Molecular Function

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Cellular Component

External links

PDB	RCSB:4pam, PDBe:4pam, PDBj:4pam
PDBsum	4pam
PubMed	25037222
UniProt	P10824\|GNAI1_RAT Guanine nucleotide-binding protein G(i) subunit alpha-1 (Gene Name=Gnai1)

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