Structure of PDB 1y3a Chain A Binding Site BS02

Receptor Information

>1y3a Chain A (length=299) Species: 9606 (Homo sapiens)

VKLLLLGAGESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIA
IIRAMGRLKIDFGDSARADDARQLFVLAMTAELAGVIKRLWKDSGVQACF
NRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTGIVETHFT
FKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVMNRMHES
MKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTY
EEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIK

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:
  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
• ChEMBL: CHEMBL384759
• DrugBank: DB04315
• ZINC: ZINC000008215481
• PDB chain: 1y3a Chain A Residue 355

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1y3a Structure of G-Alpha-I1 bound to a GDP-selective peptide provides insight into guanine nucleotide exchange
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): E43 S44 G45 K46 S47 T48 R176 R178 N269 K270 D272 L273 C325 A326
• Binding residue (residue number reindexed from 1): E10 S11 G12 K13 S14 T15 R136 R138 N223 K224 D226 L227 C279 A280
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): E43 T48 R178 D200 Q204
• Catalytic site (residue number reindexed from 1): E10 T15 R138 D160 Q164

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0001664 G protein-coupled receptor binding
• GO:0003924 GTPase activity
• GO:0003925 G protein activity
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:0010854 adenylate cyclase regulator activity
• 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: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:0007193 adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway
• GO:0007198 adenylate cyclase-inhibiting serotonin receptor signaling pathway
• GO:0034695 response to prostaglandin E
• GO:0043434 response to peptide hormone
• GO:0043949 regulation of cAMP-mediated signaling
• GO:0045542 positive regulation of cholesterol biosynthetic process
• GO:0051301 cell division
• GO:0060236 regulation of mitotic spindle organization
• GO:0072678 T cell migration
• GO:1904322 cellular response to forskolin
• GO:1904778 positive regulation of protein localization to cell cortex

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005765 lysosomal membrane
• GO:0005813 centrosome
• GO:0005829 cytosol
• GO:0005834 heterotrimeric G-protein complex
• GO:0005856 cytoskeleton
• GO:0005886 plasma membrane
• GO:0005938 cell cortex
• GO:0030496 midbody
• GO:0070062 extracellular exosome

External links

• PDB: RCSB:1y3a, PDBe:1y3a, PDBj:1y3a
• PDBsum: 1y3a
• PubMed: 16004878
• UniProt: P63096|GNAI1_HUMAN Guanine nucleotide-binding protein G(i) subunit alpha-1 (Gene Name=GNAI1)