Structure of PDB 7ytj Chain D Binding Site BS02

Receptor Information
>7ytj Chain D (length=601) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MAKFGEHLSKSLIRQYSYYYISYDDLKTELEDNLSKNNGQWTQELETDFL
ESLEIELDKVYTFCKVKHSEVFRRVKEVQEQVQHTVRLLDSNNPPTQLDF
EILEEELSDIIADVHDLAKFSRLNYTGFQKIIKKHDKKTGFILKPVFQVR
LDSKPFFKENYDELVVKISQLYDIARTSGRPFVRQTTKYWVHPDNITELK
LIILKHLPVLVFNTNKEFEREDSAITSIYFDNENLDLYYGRLRKDEGAEA
HALAWYGGMSTDTIFVERKTHREDWTGEKSVKARFALKERHVNDFLKGKY
TVDQVFAKMRKEGKKPMNEIENLEALASEIQYVMLKKKLRPVVRSFYNRT
AFQLPGDARVRISLDTELTMVREDNFDGVDRTHKNWRRTDIGVDWPFKQL
DDKDICRFPYAVLNVKLQTQLGQEPPEWVRELVGSHLVEPVPKFSKFIHG
VATLLNDKVDSIPFWLPQMDVDIRKPPLFDTQIRAPPGKTICVPVRVEPK
VYFATERTYLSWLSISILLGGVSTTLLTYGSPTAMIGSIGFFITSLAVLI
RTVMVYAKRVVNIRLKRAVDYEDKIGPGMVSVFLILSILFSFFCNLVAKL
E
Ligand information
Ligand IDIHP
InChIInChI=1S/C6H18O24P6/c7-31(8,9)25-1-2(26-32(10,11)12)4(28-34(16,17)18)6(30-36(22,23)24)5(29-35(19,20)21)3(1)27-33(13,14)15/h1-6H,(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1-,2-,3-,4+,5-,6-
InChIKeyIMQLKJBTEOYOSI-GPIVLXJGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O[P](O)(=O)O[CH]1[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]1O[P](O)(O)=O
ACDLabs 12.01
OpenEye OEToolkits 2.0.7		C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
CACTVS 3.385O[P](O)(=O)O[C@@H]1[C@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@H]1O[P](O)(O)=O
FormulaC6 H18 O24 P6
NameINOSITOL HEXAKISPHOSPHATE;
MYO-INOSITOL HEXAKISPHOSPHATE;
INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
ChEMBLCHEMBL1233511
DrugBankDB14981
ZINCZINC000169289809
PDB chain7ytj Chain D Residue 1002 [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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PDB7ytj The cytoplasmic synthesis and coupled membrane translocation of eukaryotic polyphosphate by signal-activated VTC complex.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		T199 K201 K282 S293 K295 R362 K429
Binding residue
(residue number reindexed from 1)		T186 K188 K269 S280 K282 R349 K416
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.4.1: ATP-polyphosphate phosphotransferase.
Gene Ontology
Molecular Function
GO:0000822 inositol hexakisphosphate binding
GO:0005515 protein binding
GO:0005516 calmodulin binding
GO:0008976 polyphosphate kinase activity
GO:0016740 transferase activity
Biological Process
GO:0006797 polyphosphate metabolic process
GO:0006799 polyphosphate biosynthetic process
GO:0007034 vacuolar transport
GO:0016237 microautophagy
GO:0042144 vacuole fusion, non-autophagic
GO:0061736 engulfment of target by autophagosome
Cellular Component
GO:0000329 fungal-type vacuole membrane
GO:0000421 autophagosome membrane
GO:0005737 cytoplasm
GO:0005773 vacuole
GO:0005774 vacuolar membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005938 cell cortex
GO:0016020 membrane
GO:0031410 cytoplasmic vesicle
GO:0033254 vacuolar transporter chaperone complex
GO:0071944 cell periphery

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7ytj, PDBe:7ytj, PDBj:7ytj
PDBsum7ytj
PubMed36759618
UniProtP47075|VTC4_YEAST Vacuolar transporter chaperone complex subunit 4 (Gene Name=VTC4)

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