Structure of PDB 3kuc Chain A Binding Site BS01

Receptor Information

>3kuc Chain A (length=167) Species: 9606 (Homo sapiens)

MREYKLVVLGSGGVGKSALTVQFVQGIFVDEYDPTIEDSYRKQVEVDCQQ
CMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQI
LRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLESSAKS
KINVNEIFYDLVRQINR

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: 3kuc Chain A Residue 170

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3kuc What makes Ras an efficient molecular switch: a computational, biophysical, and structural study of Ras-GDP interactions with mutants of Raf.
• Resolution: 1.92 Å
• Binding residue (original residue number in PDB): G13 V14 G15 K16 S17 A18 F28 V29 D30 Y32 N116 K117 D119 L120 S147 K149
• Binding residue (residue number reindexed from 1): G13 V14 G15 K16 S17 A18 F28 V29 D30 Y32 N116 K117 D119 L120 S147 K149
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.6.5.2: small monomeric GTPase.

Gene Ontology

Molecular Function

• GO:0003924 GTPase activity
• GO:0003925 G protein activity
• GO:0005085 guanyl-nucleotide exchange factor activity
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:0016787 hydrolase activity
• GO:0019003 GDP binding
• GO:0031267 small GTPase binding
• GO:0044877 protein-containing complex binding

Biological Process

• GO:0007165 signal transduction
• GO:0007264 small GTPase-mediated signal transduction
• GO:0007399 nervous system development
• GO:0010976 positive regulation of neuron projection development
• GO:0016079 synaptic vesicle exocytosis
• GO:0030033 microvillus assembly
• GO:0032486 Rap protein signal transduction
• GO:0038180 nerve growth factor signaling pathway
• GO:0043547 positive regulation of GTPase activity
• GO:0045860 positive regulation of protein kinase activity
• GO:0061028 establishment of endothelial barrier
• GO:0070374 positive regulation of ERK1 and ERK2 cascade
• GO:0071320 cellular response to cAMP
• GO:0072659 protein localization to plasma membrane
• GO:0098696 regulation of neurotransmitter receptor localization to postsynaptic specialization membrane
• GO:1901888 regulation of cell junction assembly
• GO:1990090 cellular response to nerve growth factor stimulus
• GO:2000301 negative regulation of synaptic vesicle exocytosis
• GO:2001214 positive regulation of vasculogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005768 endosome
• GO:0005769 early endosome
• GO:0005770 late endosome
• GO:0005829 cytosol
• GO:0005886 plasma membrane
• GO:0010008 endosome membrane
• GO:0016020 membrane
• GO:0030054 cell junction
• GO:0032045 guanyl-nucleotide exchange factor complex
• GO:0035579 specific granule membrane
• GO:0043005 neuron projection
• GO:0048471 perinuclear region of cytoplasm
• GO:0070062 extracellular exosome
• GO:0070161 anchoring junction
• GO:0097225 sperm midpiece
• GO:0098793 presynapse
• GO:0098978 glutamatergic synapse

External links

• PDB: RCSB:3kuc, PDBe:3kuc, PDBj:3kuc
• PDBsum: 3kuc
• PubMed: 20361980
• UniProt: P62834|RAP1A_HUMAN Ras-related protein Rap-1A (Gene Name=RAP1A)