Structure of PDB 5dn6 Chain D Binding Site BS01

Receptor Information
>5dn6 Chain D (length=470) Species: 266 (Paracoccus denitrificans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEANGKITQVIGAVVDVQFDGQLPAILNALETENNGKRLVLEVAQHLGEN
TVRTIAMDATEGLVRGLPVKDTGGPIMVPVGDATLGRILNVVGEPVDEGG
PVEATQTRAIHQQAPDFAAQATASEILVTGIKVIDLLAPYSKGGKIGLFG
GAGVGKTVLIMELINNIAKVHSGYSVFAGVGERTREGNDLYHEMVESGVI
KPDDLSKSQVALVYGQMNEPPGARMRVALTGLTVAEQFRDATGTDVLFFV
DNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGAMQERITSTKNGSIT
SIQAVYVPADDLTDPAPATTFAHLDATTVLSRAISELGIYPAVDPLDSNS
RILDPAVVGEEHYQVARDVQGILQKYKSLQDIIAILGMDELSEEDKLTVA
RARKIQRFLSQPFDVAKVFTGSDGVQVPLEDTIKSFKAVVAGEYDHLPEA
AFYMVGGIEDVKAKAQRLAA
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 D 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 R184 Y341 A417 F420
Binding residue
(residue number reindexed from 1)		G153 G155 K156 T157 V158 R183 Y340 A416 F419
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K157 E183 R184 R352
Catalytic site (residue number reindexed from 1) K156 E182 R183 R351
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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