Structure of PDB 1zbd Chain A Binding Site BS02

Receptor Information
>1zbd Chain A (length=177) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMFDYMFKILIIGNSSVGKTSFLFRYADDSFTPAFVSTVGIDFKVKTIY
RNDKRIKLQIWDTAGLERYRTITTAYYRGAMGFILMYDITNEESFNAVQD
WSTQIKTYSWDNAQVLLVGNKCDMEDERVVSSERGRQLADHLGFEFFEAS
AKDNINVKQTFERLVDVICEKMSESLD
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 chain1zbd Chain A Residue 303 [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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PDB1zbd Structural basis of Rab effector specificity: crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		S31 S32 V33 G34 K35 T36 S37 F47 P49 A50 F51 S53 T54 G80 N135 K136 D138 M139 S165 A166 K167
Binding residue
(residue number reindexed from 1)		S16 S17 V18 G19 K20 T21 S22 F32 P34 A35 F36 S38 T39 G65 N120 K121 D123 M124 S150 A151 K152
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001671 ATPase activator activity
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0030674 protein-macromolecule adaptor activity
GO:0030742 GTP-dependent protein binding
GO:0031489 myosin V binding
GO:0051021 GDP-dissociation inhibitor binding
GO:0051117 ATPase binding
Biological Process
GO:0001778 plasma membrane repair
GO:0003016 respiratory system process
GO:0006887 exocytosis
GO:0007005 mitochondrion organization
GO:0007274 neuromuscular synaptic transmission
GO:0007409 axonogenesis
GO:0009306 protein secretion
GO:0009791 post-embryonic development
GO:0010807 regulation of synaptic vesicle priming
GO:0014059 regulation of dopamine secretion
GO:0015031 protein transport
GO:0016079 synaptic vesicle exocytosis
GO:0016188 synaptic vesicle maturation
GO:0017156 calcium-ion regulated exocytosis
GO:0017157 regulation of exocytosis
GO:0030073 insulin secretion
GO:0030324 lung development
GO:0031630 regulation of synaptic vesicle fusion to presynaptic active zone membrane
GO:0032418 lysosome localization
GO:0032482 Rab protein signal transduction
GO:0036465 synaptic vesicle recycling
GO:0045055 regulated exocytosis
GO:0048172 regulation of short-term neuronal synaptic plasticity
GO:0048489 synaptic vesicle transport
GO:0048790 maintenance of presynaptic active zone structure
GO:0050975 sensory perception of touch
GO:0051602 response to electrical stimulus
GO:0051649 establishment of localization in cell
GO:0060478 acrosomal vesicle exocytosis
GO:0061670 evoked neurotransmitter secretion
GO:0097091 synaptic vesicle clustering
GO:0099161 regulation of presynaptic dense core granule exocytosis
GO:1903307 positive regulation of regulated secretory pathway
GO:1905684 regulation of plasma membrane repair
GO:2000300 regulation of synaptic vesicle exocytosis
Cellular Component
GO:0001669 acrosomal vesicle
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005768 endosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0008021 synaptic vesicle
GO:0030133 transport vesicle
GO:0030141 secretory granule
GO:0030424 axon
GO:0030672 synaptic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0032991 protein-containing complex
GO:0042995 cell projection
GO:0043195 terminal bouton
GO:0045202 synapse
GO:0048471 perinuclear region of cytoplasm
GO:0048786 presynaptic active zone
GO:0098793 presynapse
GO:0098794 postsynapse
GO:0099503 secretory vesicle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1zbd, PDBe:1zbd, PDBj:1zbd
PDBsum1zbd
PubMed10025402
UniProtP63012|RAB3A_RAT Ras-related protein Rab-3A (Gene Name=Rab3a)

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