Structure of PDB 7tao Chain A Binding Site BS01

Receptor Information

>7tao Chain A (length=750) Species: 4932 (Saccharomyces cerevisiae)

EKEEAIFRSAEMALVQFYIPQEISRDSAYTLGQLGLVQFRDLNSKVRAFQ
RTFVNEIRRLDNVERQYRYFYSLLKKHDIKLYEGDTDKYLDGSGELYVPP
SGSVIDDYVRNASYLEERLIQMEDATDQIEVQKNDLEQYRFILQSGDEFF
LKVNYVTGVIARDKVATLEQILWRVLRGNLFFKTVEIEQPVYDVKTREYK
HKNAFIVFSHGDLIIKRIRKIAESLDANLYDVDSSNEGRSQQLAKVNKNL
SDLYTVLKTTSTTLESELYAIAKELDSWFQDVTREKAIFEILNKSNYDTN
RKILIAEGWIPRDELATLQARLGEMIARLGIDVPSIIQVLDTNHTPPTFH
RTNKFTAGFQSICDCYGIAQYREINAGLPTIVTFPFMFAIMFGDMGHGFL
MTLAALSLVLNEKKINKMKRGEIFDMAFTGRYIILLMGVFSMYTGFLYND
IFSKTMTIFKSGWKWPDHWKKGESITATSVGTYPIGLDWAWHGTENALLF
SNSYKMKLSILMGFIHMTYSYFFSLANHLYFNSMIDIIGNFIPGLLFMQG
IFGYLSVCIVYKWAVDWVKDGKPAPGLLNMLINMFLSPGTIDDELYPHQA
KVQVFLLLMALVCIPWLLLVKPLHFKFTEDFGDIMIHQVIHTIEFCLNCV
SHTASYLRLWALSLAHAQLSSVLWTMTIQIAFGFRGFVGVFMTVALFAMW
FALTCAVLVLMEGTSAMLHSLRLHWVESMSKFFVGEGLPYEPFAFEYKDM

Ligand information

• Ligand ID: WEV
• InChI: InChI=1S/C35H58O9/c1-19(2)32-24(7)27(36)18-35(40,44-32)26(9)31(38)25(8)33-28(41-10)14-12-13-20(3)15-22(5)30(37)23(6)16-21(4)17-29(42-11)34(39)43-33/h12-14,16-17,19,22-28,30-33,36-38,40H,15,18H2,1-11H3/b14-12+,20-13+,21-16+,29-17-/t22-,23-,24+,25+,26+,27-,28+,30+,31-,32-,33-,35-/m1/s1
• InChIKey: XDHNQDDQEHDUTM-XJKSCTEHSA-N
• SMILES:
  CACTVS 3.385: CO[C@H]1/C=C/C=C(C)/C[C@@H](C)[C@H](O)[C@H](C)\C=C(C)\C=C(OC)\C(=O)O[C@@H]1[C@@H](C)[C@@H](O)[C@H](C)[C@@]2(O)C[C@@H](O)[C@H](C)[C@H](O2)C(C)C
  ACDLabs 12.01: COC1C=CC=C(CC(C)C(C(C=C(C=C(C(OC1C(C)C(O)C(C)C2(CC(O)C(C(O2)C(C)C)C)O)=O)OC)C)C)O)C
  OpenEye OEToolkits 2.0.7: CC1CC(=CC=CC(C(OC(=O)C(=CC(=CC(C1O)C)C)OC)C(C)C(C(C)C2(CC(C(C(O2)C(C)C)C)O)O)O)OC)C
  CACTVS 3.385: CO[CH]1C=CC=C(C)C[CH](C)[CH](O)[CH](C)C=C(C)C=C(OC)C(=O)O[CH]1[CH](C)[CH](O)[CH](C)[C]2(O)C[CH](O)[CH](C)[CH](O2)C(C)C
  OpenEye OEToolkits 2.0.7: C[C@@H]1C/C(=C/C=C/[C@@H]([C@H](OC(=O)/C(=C/C(=C/[C@H]([C@H]1O)C)/C)/OC)[C@@H](C)[C@H]([C@H](C)[C@]2(C[C@H]([C@@H]([C@H](O2)C(C)C)C)O)O)O)OC)/C
• Formula: C35 H58 O9
• Name: (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-10-hydroxy-3,15-dimethoxy-7,9,11,13-tetramethyl-16-oxo-1-oxacyclohexadeca-4,6,12,14-tetraen-2-yl]pentan-2-yl}-4-methyl-5-propan-2-yl-alpha-D-threo-pentopyranose
• PDB chain: 7tao Chain D Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7tao Cryo-EM of the Yeast V O Complex Reveals Distinct Binding Sites for Macrolide V-ATPase Inhibitors.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): I713 V716 I720
• Binding residue (residue number reindexed from 1): I636 V639 I643
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0046961 proton-transporting ATPase activity, rotational mechanism
• GO:0051117 ATPase binding
• GO:0080025 phosphatidylinositol-3,5-bisphosphate binding

Biological Process

• GO:0006797 polyphosphate metabolic process
• GO:0007035 vacuolar acidification
• GO:0065003 protein-containing complex assembly
• GO:0071469 cellular response to alkaline pH
• GO:0071474 cellular hyperosmotic response
• GO:1902600 proton transmembrane transport
• GO:1903778 protein localization to vacuolar membrane

Cellular Component

• GO:0000220 vacuolar proton-transporting V-type ATPase, V0 domain
• GO:0000324 fungal-type vacuole
• GO:0000329 fungal-type vacuole membrane
• GO:0005773 vacuole
• GO:0005774 vacuolar membrane
• GO:0016020 membrane
• GO:0016471 vacuolar proton-transporting V-type ATPase complex
• GO:0033179 proton-transporting V-type ATPase, V0 domain
• GO:0045121 membrane raft

External links

• PDB: RCSB:7tao, PDBe:7tao, PDBj:7tao
• PDBsum: 7tao
• PubMed: 35148071
• UniProt: P32563|VPP1_YEAST V-type proton ATPase subunit a, vacuolar isoform (Gene Name=VPH1)