Structure of PDB 5dn6 Chain F Binding Site BS01

Receptor Information
>5dn6 Chain F (length=466) Species: 266 (Paracoccus denitrificans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ANGKITQVIGAVVDVQFDGQLPAILNALETENNGKRLVLEVAQHLGENTV
RTIAMDATEGLVRGLPVKDTGGPIMVPVGDATLGRILNVVGEPVDEGGPV
EATQTRAIHQQAPDFAAQATASEILVTGIKVIDLLAPYSKGGKIGLFGGA
GVGKTVLIMELINNIAKVHSGYSVFAGVGERTREGNDLYHEMVESGVIKP
DDLSKSQVALVYGQMNEPPGARMRVALTGLTVAEQFRDATGTDVLFFVDN
IFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGAMQERITSTKNGSITSI
QAVYVPADDLTDPAPATTFAHLDATTVLSRAISELGIYPAVDPLDSNSRI
LDPAVVGEEHYQVARDVQGILQKYKSLQDIIAILGMDELSEEDKLTVARA
RKIQRFLSQPFDVAKVFTGSDGVQVPLEDTIKSFKAVVAGEYDHLPEAAF
YMVGGIEDVKAKAQRL
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[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
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain5dn6 Chain F Residue 600 [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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PDB5dn6 Structure of ATP synthase from Paracoccus denitrificans determined by X-ray crystallography at 4.0 angstrom resolution.
Resolution3.98 Å
Binding residue
(original residue number in PDB)		G154 G156 K157 T158 V159 E183 Y341 F414 F420
Binding residue
(residue number reindexed from 1)		G151 G153 K154 T155 V156 E180 Y338 F411 F417
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K157 E183 R184 R352
Catalytic site (residue number reindexed from 1) K154 E180 R181 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:0046034 ATP metabolic process
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005886 plasma membrane
GO:0045259 proton-transporting ATP synthase complex
GO:0045261 proton-transporting ATP synthase complex, catalytic core F(1)

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5dn6, PDBe:5dn6, PDBj:5dn6
PDBsum5dn6
PubMed26460036
UniProtA1B8P0|ATPB_PARDP ATP synthase subunit beta (Gene Name=atpD)

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