Structure of PDB 7kyb Chain A Binding Site BS01

Receptor Information

>7kyb Chain A (length=957) Species: 559292 (Saccharomyces cerevisiae S288C)

TFLPKNILFQFHNFANVYFLVLIILGAFQIFGVTNPGLSAVPLVVIVIIT
AIKDAIEDSRRTVPTKKSRISRELNFSVVINFVLLFILCFVSGIANGVYY
DKKGRSRFSYEFGTIAGSAATNGFVSFWVAVILYQSLVPISLYISVEIIK
TAQAAFIYGDVLLYNAKLDYPCTPKSWNISDDLGQVEYIFSDKTGTLTQN
VMEFKKCTINGVSYGRAYTEALAGLRKRQGIDVETEGRREKAEIAKDRDT
MIDELRALSGNSQFYPEEVTFVSKEFVRDLKGASGEVQQRCCEHFMLALA
LCHSVLVEANPDNPKKLDLKAQSPDEAALVATARDVGFSFVGKTKKGLII
EMQGIQKEFEILNILEFNSSRKRMSCIVKIPGEPRALLICKGADSIIYSR
LSRQSNSEAILEKTALHLEQYATEGLRTLCIAQRELSWSEYEKWNEKYDI
AAASLANREDELEVVADSIERELILLGGTAIEDRLQDGVPDCIELLAEAG
IKLWVLTGDKVETAINIGFSCNLLNNEMELLVIKTTGDDVKEFGSEPSEI
VDALLSKYLKEYFNLTGSEEEIFEAKKDHEFPKGNYAIVIDGDALKLALY
GEDIRRKFLLLCKNCRAVLCCRVSPSQKAAVVKLVKDSLDVMTLAIGDGS
NDVAMIQSADVGIGIAGEEGRQAVMCSDYAIGQFRYLARLVLVHGRWSYK
RLAEMIPEFFYKNMIFALALFWYGIYNDFDGSYLYEYTYMMFYNLAFTSL
PVIFLGILDQDVNDTISLVVPQLYRVGILRKEWNQRKFLWYMLDGLYQSI
ICFFFPYLVYHKNMIVTSNGLGLDHRYFVGVYVTTIAVISCNTYVLLHQY
RWDWFSGLFIALSCLVVFAWTGIWSSAIASREFFKAAARIYGAPSFWAVF
FVAVLFCLLPRFTYDSFQKFFYPTDVEIVREMWQHGHFDHYPPGYDPTDP
NRPKVTK

Ligand information

• Ligand ID: ADP
• InChI: InChI=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
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(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 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 7kyb Chain A Residue 1602

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7kyb Transport mechanism of P4 ATPase phosphatidylcholine flippases.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): D667 T669 S798 E801 F842 S844 K871 R909 L911 R1104
• Binding residue (residue number reindexed from 1): D192 T194 S323 E326 F367 S369 K391 R427 L429 R622
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 7.6.2.1: P-type phospholipid transporter.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0000287 magnesium ion binding
• GO:0005215 transporter activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0016887 ATP hydrolysis activity
• GO:0042802 identical protein binding
• GO:0046872 metal ion binding
• GO:0090554 phosphatidylcholine floppase activity
• GO:0090555 phosphatidylethanolamine flippase activity
• GO:0090556 phosphatidylserine floppase activity
• GO:0140326 ATPase-coupled intramembrane lipid transporter activity
• GO:0140345 phosphatidylcholine flippase activity
• GO:0140346 phosphatidylserine flippase activity
• GO:0140351 glycosylceramide flippase activity

Biological Process

• GO:0006869 lipid transport
• GO:0006886 intracellular protein transport
• GO:0006897 endocytosis
• GO:0007163 establishment or maintenance of cell polarity
• GO:0015914 phospholipid transport
• GO:0045332 phospholipid translocation
• GO:0099040 ceramide translocation
• GO:0140331 aminophospholipid translocation

Cellular Component

• GO:0005739 mitochondrion
• GO:0005768 endosome
• GO:0005783 endoplasmic reticulum
• GO:0005794 Golgi apparatus
• GO:0005886 plasma membrane
• GO:0005933 cellular bud
• GO:0005935 cellular bud neck
• GO:0010008 endosome membrane
• GO:0016020 membrane
• GO:0030428 cell septum
• GO:0070867 mating projection tip membrane
• GO:0071944 cell periphery
• GO:1990531 phospholipid-translocating ATPase complex

External links

• PDB: RCSB:7kyb, PDBe:7kyb, PDBj:7kyb
• PDBsum: 7kyb
• PubMed: 33320091
• UniProt: P32660|ATC5_YEAST Phospholipid-transporting ATPase DNF1 (Gene Name=DNF1)