Structure of PDB 7tmm Chain B Binding Site BS01

Receptor Information
>7tmm Chain B (length=464) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NKKAVEQGFNVKPRLNYNTVSGVNGPLVILEKVKFPRYNEIVNLTLPDGT
VRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGR
IFDGSGRPIDNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTM
NSIARGQKIPIFSASGLPHNEIAAQICRQAGLVRPNFSIVFAAMGVNLET
ARFFKQDFEENGSLERTSLFLNLANDPTIERIITPRLALTTAEYLAYQTE
RHVLTILTDMSSYADALREVSAAREEVPGRRGYPGYMYTDLSTIYERAGR
VEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFVDRQLHNKGIYP
PINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVVG
EEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKE
MLNRISPKILDEFY
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain7tmm Chain A Residue 701 [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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PDB7tmm Coordinated conformational changes in the V 1 complex during V-ATPase reversible dissociation.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		R381 K384
Binding residue
(residue number reindexed from 1)		R360 K363
Annotation score5
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0046961 proton-transporting ATPase activity, rotational mechanism
Biological Process
GO:0000425 pexophagy
GO:0006874 intracellular calcium ion homeostasis
GO:0007035 vacuolar acidification
GO:0046034 ATP metabolic process
GO:0048388 endosomal lumen acidification
GO:0055085 transmembrane transport
GO:0061795 Golgi lumen acidification
GO:1902600 proton transmembrane transport
GO:1902906 proteasome storage granule assembly
Cellular Component
GO:0000139 Golgi membrane
GO:0000221 vacuolar proton-transporting V-type ATPase, V1 domain
GO:0000329 fungal-type vacuole membrane
GO:0005737 cytoplasm
GO:0005773 vacuole
GO:0005774 vacuolar membrane
GO:0010494 cytoplasmic stress granule
GO:0016020 membrane
GO:0016471 vacuolar proton-transporting V-type ATPase complex
GO:0033176 proton-transporting V-type ATPase complex
GO:0033180 proton-transporting V-type ATPase, V1 domain
GO:0045121 membrane raft
GO:1990816 vacuole-mitochondrion membrane contact site

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7tmm, PDBe:7tmm, PDBj:7tmm
PDBsum7tmm
PubMed35469063
UniProtP16140|VATB_YEAST V-type proton ATPase subunit B (Gene Name=VMA2)

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