Structure of PDB 3tkl Chain A Binding Site BS02

Receptor Information
>3tkl Chain A (length=171) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIEL
DGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQW
LQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSA
KNATNVEQSFMTMAAEIKKRM
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 chain3tkl Chain A Residue 301 [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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PDB3tkl Structural insights into a unique Legionella pneumophila effector LidA recognizing both GDP and GTP bound Rab1 in their active state
Resolution2.183 Å
Binding residue
(original residue number in PDB)		S20 G21 G23 K24 S25 C26 Y36 E38 Y40 T43 G69 N124 K125 D127 L128 S154 A155 K156
Binding residue
(residue number reindexed from 1)		S15 G16 G18 K19 S20 C21 Y31 E33 Y35 T38 G64 N119 K120 D122 L123 S149 A150 K151
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Q70
Catalytic site (residue number reindexed from 1) Q65
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:0045296 cadherin binding
Biological Process
GO:0000045 autophagosome assembly
GO:0006886 intracellular protein transport
GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport
GO:0006897 endocytosis
GO:0006914 autophagy
GO:0007030 Golgi organization
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0016477 cell migration
GO:0019068 virion assembly
GO:0030252 growth hormone secretion
GO:0032402 melanosome transport
GO:0032757 positive regulation of interleukin-8 production
GO:0034446 substrate adhesion-dependent cell spreading
GO:0042742 defense response to bacterium
GO:0047496 vesicle transport along microtubule
GO:0060271 cilium assembly
GO:0090110 COPII-coated vesicle cargo loading
GO:0090557 establishment of endothelial intestinal barrier
GO:1903020 positive regulation of glycoprotein metabolic process
Cellular Component
GO:0000139 Golgi membrane
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005769 early endosome
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0012505 endomembrane system
GO:0016020 membrane
GO:0030658 transport vesicle membrane
GO:0042470 melanosome
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3tkl, PDBe:3tkl, PDBj:3tkl
PDBsum3tkl
PubMed22416225
UniProtP62820|RAB1A_HUMAN Ras-related protein Rab-1A (Gene Name=RAB1A)

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