Structure of PDB 6ynz Chain D4 Binding Site BS01

Receptor Information
>6ynz Chain D4 (length=470) Species: 5911 (Tetrahymena thermophila) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KANGQVSQVIGAVVDVQFEGELPQILNALEVQGTQHRLVLEVAQHLGDSR
VRTIAMDSTEGLVRGQPVVDTGLPISVPVGPGTLGRIMNVIGEPIDQRGP
IKAAKLYPIHRDAPSFTDQATSAEILVTGIKVVDLLAPYARGGKIGLFGG
AGVGKTVLIQELINNVAKHHGGYSVFAGVGERTREGNDLYHEMMDSKVIS
VKEGESRCALIFGQMNEPPGARARVGLTGLTVAEYFRDEEGKDVLLFVDN
IFRFTQACSEVSALLGRIPSAVGYQPTLATDLGALQERITTTQKGSITSV
QAIYVPADDLTDPAPATTFAHLDATTVLNRGLTELGIYPAVDPLDSTSRM
LDPITIGEEHYTVARGVQKLLQDYKSLQDIIAILGVDDLSEEDKLVVARA
RKVQKFLSQPFFMSEVFSGIPGRFVNLKQNIASFKALLEGAGDEYPESCF
YMKGDLEESLAAGRADALKS
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 chain6ynz Chain D4 Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6ynz Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		G180 K181 T182 V183 E211 Y364 F437 S440 F443
Binding residue
(residue number reindexed from 1)		G154 K155 T156 V157 E185 Y338 F411 S414 F417
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K181 E207 R208 R375
Catalytic site (residue number reindexed from 1) K155 E181 R182 R349
Enzyme Commision number 7.1.2.2: H(+)-transporting two-sector ATPase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism
GO:0046961 proton-transporting ATPase activity, rotational mechanism
Biological Process
GO:0006754 ATP biosynthetic process
GO:0015986 proton motive force-driven ATP synthesis
GO:0042776 proton motive force-driven mitochondrial ATP synthesis
GO:0046034 ATP metabolic process
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005739 mitochondrion
GO:0009507 chloroplast
GO:0016020 membrane
GO:0045261 proton-transporting ATP synthase complex, catalytic core F(1)

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6ynz, PDBe:6ynz, PDBj:6ynz
PDBsum6ynz
PubMed33093501
UniProtI7LZV1

[Back to BioLiP]