Structure of PDB 7rd8 Chain A Binding Site BS01

Receptor Information

>7rd8 Chain A (length=929) Species: 4932 (Saccharomyces cerevisiae)

EREIHPDTTPVYDRNRYVSNELSNAKYNAVTFVPTLLYEQFKFFYNLYFL
VVALSQAVPALRIGYLSSYIVPLAFVLTVTMAKEAIDDIQRRRRDRESNN
ELYHVITRNRSIPSKDLKVGDLIKVHKGDRIPADLVLLQSSEPSGESFIK
TDQLDGETDWKLRVACPLTQNLINRISITASAPEKSIHKFLGKVTYKDST
SNPLSVDNTLWANTVLASSGFCIACVVYTGRDTRQAMNTTTAKVKTGLLE
LEINSISKILCACVFALSILLVAFAGFHNDDWYIDILRYLILFSTIIPVS
LRVNLDLAKSVYAHQIEHDKTIPETIVRTSTIPEDLGRIEYLLSDKTGTL
TQNDMQLKKIHLGTVSYTSETLDIVSDYVQSLVKDMSFRVRDMILTLAIC
HNVTPTFEDDELTYQAASPDEIAIVKFTESVGLSLFKRDRHSISLLHEHS
GKTLNYEILQVFPFNSDSKRMGIIVRDEQLDEYWFMQKGADTVMSKIVES
NDWLEEETGNMAREGLRTLVIGRKKLNKKIYEQFQKEITKYLEHDLELLG
LTGVEDKLQKDVKSSIELLRNAGIKIWMLTGDKVETARCVSISAKLISRG
QYVHTITKVACLLIDGESLGMFLKHYEQEFFDVVVHLPTVIACRCTPQQK
ADVALVIRKMTGKRVCCIGDGGNDVSMIQCADVGVGIVGKEGKQASLAAD
FSITQFCHLTELLLWHGRNSYKRSAKLAQFVMHRGLIIAICQAVYSICSL
FEPIALYQGWLMVGYATCYTMAPVFSLTLDHDIEESLTKIYPELYKELTE
GKSLSYKTFFVWVLLSLFQGSVIQLFSQAFTSLLDTDFTRMVAISFTALV
VNELIMVALEIYTWNKTMLVTEIATLLFYIVSVPFLGDYFDLGYMTTVNY
YAGLLVILLISIFPVWTAKAIYRRLHPPS

Ligand information

• Ligand ID: ACP
• InChI: InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
• InChIKey: UFZTZBNSLXELAL-IOSLPCCCSA-N
• SMILES:
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(CP(=O)(O)O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C11 H18 N5 O12 P3
• Name: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
  ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
• ChEMBL: CHEMBL133463
• DrugBank: DB03909
• ZINC: ZINC000008295124
• PDB chain: 7rd8 Chain A Residue 1201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7rd8 Structural basis of the P4B ATPase lipid flippase activity.
• Resolution: 5.64 Å
• Binding residue (original residue number in PDB): T505 F640 K645
• Binding residue (residue number reindexed from 1): T347 F464 K469
• Annotation score: 3

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:0046872 metal ion binding
• GO:0090555 phosphatidylethanolamine flippase activity
• GO:0090556 phosphatidylserine floppase activity
• GO:0140326 ATPase-coupled intramembrane lipid transporter activity
• GO:0140346 phosphatidylserine flippase activity
• GO:0180013 lysophosphatidylserine flippase activity

Biological Process

• GO:0006869 lipid transport
• GO:0006890 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
• GO:0006897 endocytosis
• GO:0007033 vacuole organization
• GO:0015031 protein transport
• GO:0015914 phospholipid transport
• GO:0045332 phospholipid translocation
• GO:0098629 trans-Golgi network membrane organization
• GO:0140331 aminophospholipid translocation

Cellular Component

• GO:0000139 Golgi membrane
• GO:0005768 endosome
• GO:0005770 late endosome
• GO:0005794 Golgi apparatus
• GO:0005802 trans-Golgi network
• GO:0005886 plasma membrane
• GO:0010008 endosome membrane
• GO:0016020 membrane

External links

• PDB: RCSB:7rd8, PDBe:7rd8, PDBj:7rd8
• PDBsum: 7rd8
• PubMed: 34645814
• UniProt: P40527|ATC7_YEAST Phospholipid-transporting ATPase NEO1 (Gene Name=NEO1)