Structure of PDB 5lef Chain B Binding Site BS01

Receptor Information
>5lef Chain B (length=159) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIGIDFLSKTMDRTVRLQL
WDTAGLERFRSLIPSYIRDSTVAVVVYDITNVNSFQQTTKWIDDVRTERG
SDVIIMLVGNKTDLADKRQVSIEEGERKAKELNVMFIETSAKAGYNVKQL
FRRVAAALP
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain5lef Chain B Residue 201 [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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PDB5lef Coupling fission and exit of RAB6 vesicles at Golgi hotspots through kinesin-myosin interactions.
Resolution2.088 Å
Binding residue
(original residue number in PDB)		Q22 S23 V24 G25 K26 T27 S28 F38 D39 N40 Y42 A44 T45 G71 K127 D129 L130 S156 K158
Binding residue
(residue number reindexed from 1)		Q9 S10 V11 G12 K13 T14 S15 F25 D26 N27 Y29 A31 T32 G55 K111 D113 L114 S140 K142
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0019904 protein domain specific binding
GO:0031489 myosin V binding
Biological Process
GO:0006886 intracellular protein transport
GO:0006890 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
GO:0006891 intra-Golgi vesicle-mediated transport
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0018125 peptidyl-cysteine methylation
GO:0019882 antigen processing and presentation
GO:0031175 neuron projection development
GO:0034067 protein localization to Golgi apparatus
GO:0034498 early endosome to Golgi transport
GO:0042147 retrograde transport, endosome to Golgi
GO:0072385 minus-end-directed organelle transport along microtubule
GO:1903292 protein localization to Golgi membrane
Cellular Component
GO:0000139 Golgi membrane
GO:0002080 acrosomal membrane
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0012505 endomembrane system
GO:0016020 membrane
GO:0030667 secretory granule membrane
GO:0031410 cytoplasmic vesicle
GO:0032588 trans-Golgi network membrane
GO:0070062 extracellular exosome
GO:0070381 endosome to plasma membrane transport vesicle

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5lef, PDBe:5lef, PDBj:5lef
PDBsum5lef
PubMed29093437
UniProtP20340|RAB6A_HUMAN Ras-related protein Rab-6A (Gene Name=RAB6A)

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