Structure of PDB 4xd7 Chain F Binding Site BS01

Receptor Information
>4xd7 Chain F (length=464) Species: 2334 (Bacillus sp. PS3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRVIQVMGPVVDVKFNGHLPIYNALKIQHKARNENEVDIDLTLEVALHLG
DDTVRTIAMASTDGLIRGMEVIDTGAPISVPVGEVTLGRVFNVLGEPIDL
EGDIPADARRDPIHRPAPKFEELATEVEILETGIKVVDLLAPYIKGGKIG
LFGGAGVGKTVLIQELIHNIAQEHGGISVFAGVGERTREGNDLYHEMKDS
GVISKTAMVFGQMNEPPGARMRVALTGLTMAEYFRDEQQDVLLFIDNIFR
FTQAGSEVSALLGRMPSAVGYQPTLATEMGQLQERITSTAKGSITSIQAI
YVPADDYTDPAPATTFSHLDATTNLERKLAEMGIYPAVDPLASTSRALAP
EIVGEEHYQVARKVQQTLQRYKELQDIIAILGMDELSDEDKLVVHRARRI
QFFLSQNFHVAEQFTGQPGSYVPVKETVRGFKEILEGKYDHLPEDAFRLV
GRIEEVVEKAKAMG
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 chain4xd7 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

[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]
PDB4xd7 Structure of a thermophilic F1 -ATPase inhibited by an epsilon-subunit: deeper insight into the epsilon-inhibition mechanism.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		G161 V162 G163 K164 T165 V166 Y341 F420
Binding residue
(residue number reindexed from 1)		G156 V157 G158 K159 T160 V161 Y335 F414
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K164 E190 R191 R352
Catalytic site (residue number reindexed from 1) K159 E185 R186 R346
Enzyme Commision number 7.1.2.2: H(+)-transporting two-sector ATPase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
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)

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4xd7, PDBe:4xd7, PDBj:4xd7
PDBsum4xd7
PubMed26032434
UniProtP07677|ATPB_BACP3 ATP synthase subunit beta (Gene Name=atpD)

[Back to BioLiP]