Structure of PDB 5dn6 Chain C Binding Site BS01

Receptor Information
>5dn6 Chain C (length=484) Species: 266 (Paracoccus denitrificans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VGQVLSVGDGIARVYGLDKVQAGEMVEFPGGIRGMVLNLETDNVGVVIFG
DDRDIKEGDTVKRTGAIVEVPAGKELLGRVVDALGNPIDGKGPLNASERR
IADVKAPGIMPRKSVHEPMATGLKSVDAMIPVGRGQRELIIGDRQTGKTA
IALDTILNQANYNGREADGMKTLHCIYVAVGQKRSTVAQLVKKLEETGAM
AYTTVVAATASDPAPMQYLAPYSATAMGEYFRDNGMDALIIYDDLSKQAV
AYRQMSLLLRRPPGREAYPGDVFYLHSRLLERSAKLNEANGAGSLTALPI
IETQAGDVSAYIPTNVISITDGQIFLETELFFQGIRPAVNTGLSVSRVGS
AAQTKAMKSVAGPVKLELAQYREMAAFAQFGSDLDAATQKLLNRGARLTE
LMKQPQYSPLTNAEIVIVIYAGTKGYLDGIPVRDVTKWEHGLLQYLRNQK
ADLLEDMTKNDRKVAGELEDAIKAALDGYAKTYA
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 C 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)		Q172 G174 K175 T176 A177 R363 Q431 Q433
Binding residue
(residue number reindexed from 1)		Q145 G147 K148 T149 A150 R336 Q404 Q406
Annotation score5
Enzymatic activity
Enzyme Commision number 7.1.2.2: H(+)-transporting two-sector ATPase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0032559 adenyl ribonucleotide binding
GO:0043531 ADP binding
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
UniProtA1B8N8|ATPA_PARDP ATP synthase subunit alpha (Gene Name=atpA)

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