Structure of PDB 6s5h Chain A Binding Site BS01

Receptor Information
>6s5h Chain A (length=175) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMQAPHKEHLYKLLVIGDLGVGKTSIIKRYVHQNFSSHYRATIGVDFALK
VLHWDPETVVRLQLWDIAGQERFGNMTRVYYREAMGAFIVFDVTRPATFE
AVAKWKNDLDSKLSLPNGKPVSVVLLANKCDQNGLKMDQFCKEHGFVGWF
ETSAKENINIDEASRCLVKHILANE
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 chain6s5h 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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PDB6s5h Structure of the human RAB38 in complex with GTP
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L18 G19 V20 G21 K22 T23 S24 F34 S36 Y38 A40 T41 G68 K128 D130 S159 K161
Binding residue
(residue number reindexed from 1)		L19 G20 V21 G22 K23 T24 S25 F35 S37 Y39 A41 T42 G69 K129 D131 S153 K155
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0030742 GTP-dependent protein binding
GO:0035612 AP-2 adaptor complex binding
GO:0035650 AP-1 adaptor complex binding
GO:0035651 AP-3 adaptor complex binding
GO:0036461 BLOC-2 complex binding
Biological Process
GO:0006886 intracellular protein transport
GO:0007005 mitochondrion organization
GO:0007264 small GTPase-mediated signal transduction
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0032438 melanosome organization
GO:0035646 endosome to melanosome transport
GO:0048023 positive regulation of melanin biosynthetic process
GO:0060155 platelet dense granule organization
GO:0072657 protein localization to membrane
GO:0090383 phagosome acidification
GO:1903232 melanosome assembly
GO:1904377 positive regulation of protein localization to cell periphery
GO:2001247 positive regulation of phosphatidylcholine biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005764 lysosome
GO:0005769 early endosome
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0012505 endomembrane system
GO:0016020 membrane
GO:0030670 phagocytic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0031905 early endosome lumen
GO:0031982 vesicle
GO:0033162 melanosome membrane
GO:0042470 melanosome
GO:0043231 intracellular membrane-bounded organelle
GO:0044233 mitochondria-associated endoplasmic reticulum membrane contact site
GO:0044297 cell body
GO:0045335 phagocytic vesicle
GO:0048471 perinuclear region of cytoplasm

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6s5h, PDBe:6s5h, PDBj:6s5h
PDBsum6s5h
PubMed
UniProtP57729|RAB38_HUMAN Ras-related protein Rab-38 (Gene Name=RAB38)

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