Structure of PDB 8e0a Chain B Binding Site BS01

Receptor Information
>8e0a Chain B (length=176) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRVPTLHPTSEELTI
AGMTFTTFDLGRVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDE
TIANVPILILGNKIDRPEAISEERLREMFGLYGQTTGKGSISLKELNARP
LEVFMCSVLKRQGYGEGFRWMAQYID
Ligand information
Ligand IDGDP
InChIInChI=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
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=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 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(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
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain8e0a Chain B Residue 204 [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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PDB8e0a The alarmone ppGpp selectively inhibits the isoform A of the human small GTPase Sar1.
Resolution1.797 Å
Binding residue
(original residue number in PDB)		N35 G37 K38 T39 T40 H58 N134 K135 D137 R138 S179 L181
Binding residue
(residue number reindexed from 1)		N23 G25 K26 T27 T28 H42 N112 K113 D115 R116 S157 L159
Annotation score4
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:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
GO:0140785 amino acid sensor activity
Biological Process
GO:0002474 antigen processing and presentation of peptide antigen via MHC class I
GO:0003400 regulation of COPII vesicle coating
GO:0006886 intracellular protein transport
GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport
GO:0015031 protein transport
GO:0016050 vesicle organization
GO:0016192 vesicle-mediated transport
GO:0032368 regulation of lipid transport
GO:0042953 lipoprotein transport
GO:0048208 COPII vesicle coating
GO:0055088 lipid homeostasis
GO:0061024 membrane organization
GO:0070863 positive regulation of protein exit from endoplasmic reticulum
GO:0090110 COPII-coated vesicle cargo loading
GO:0140353 lipid export from cell
GO:1903432 regulation of TORC1 signaling
GO:1904262 negative regulation of TORC1 signaling
GO:1990253 cellular response to leucine starvation
Cellular Component
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0012507 ER to Golgi transport vesicle membrane
GO:0016020 membrane
GO:0030127 COPII vesicle coat
GO:0032580 Golgi cisterna membrane
GO:0070971 endoplasmic reticulum exit site

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8e0a, PDBe:8e0a, PDBj:8e0a
PDBsum8e0a
PubMed36369712
UniProtQ9Y6B6|SAR1B_HUMAN Small COPII coat GTPase SAR1B (Gene Name=SAR1B)

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