Structure of PDB 5knc Chain F Binding Site BS01

Receptor Information
>5knc Chain F (length=455) Species: 768486 (Enterococcus hirae ATCC 9790) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIKEYRTIKEVVGPLMAVEKVSGVKYEELIEVRMQNGEIRRGQVLEVQED
KAMVQIFEGTSGINLKNSSVRFLGHPLQLGVSEDMIGRVFDGLGRPKDNG
PEILPEKYLDINGEVINPIARDYPDEFIQTGISAIDHLNTLVRGQKLPVF
SGSGLPHKELAAQIARQATVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQ
TGAIDRSVMFMNLANDPAIERIATPRMALTAAEYLAYEKGMHVLVIMTDM
TNYAEALREISAARREVPGRRGYPGYLYTNLATLFERAGRIRGLKGSVTQ
IPILTMPEDDKTHPIPDLTGYITEGQIILTRELYKSGIQPPIDVLPSLSR
LKDKGTGAGKTREDHAATMNQLFAAYAQGKQAKELAVVLGESALSDIDKI
YAKFAERFENEYVNQGFYTNRTITETLDLGWELLAMLPRTELKRIKDDLL
DKYLP
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 chain5knc Chain C Residue 602 [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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PDB5knc Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor
Resolution3.015 Å
Binding residue
(original residue number in PDB)
R350 D353
Binding residue
(residue number reindexed from 1)
R350 D353
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) H157 I186 T187 R350
Catalytic site (residue number reindexed from 1) H157 I186 T187 R350
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism
Biological Process
GO:0006814 sodium ion transport
GO:0042777 proton motive force-driven plasma membrane ATP synthesis
GO:0046034 ATP metabolic process
GO:1902600 proton transmembrane transport

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Molecular Function

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Biological Process
External links
PDB RCSB:5knc, PDBe:5knc, PDBj:5knc
PDBsum5knc
PubMed27807367
UniProtQ08637|NTPB_ENTHA V-type sodium ATPase subunit B (Gene Name=ntpB)

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