Structure of PDB 7pem Chain A Binding Site BS03

Receptor Information

>7pem Chain A (length=1066) Species: 559292 (Saccharomyces cerevisiae S288C)

PRVIHINDSLANSSFGYSDNHISTTKYNFATFLPKFLFQEFSKYANLFFL
CTSAIQQVPHVSPTNRYTTIGTLLVVLIVSAMKECIEDIKRANSDKELNN
STAEIFSEAHDDFVEKRWIDIRVGDIIRVKSEEPIPADTIILSSSEPEGL
CYIETANLDGETNLKIKQSRVETAKFIDVKTLKNMNGKVVSEQPNSSLYT
YEGTMTLNDRQIPLSPDQMILRGATLRNTAWIFGLVIFTGHETKLLRNAT
ATPIKRTAVEKIINRQIIALFTVLIVLILISSIGNVIMSTADAKHLSYLY
LEGTNKAGLFFKDFLTFWILFSNLVPISLFVTVELIKYYQAFMIGSDLDL
YYEKTDTPTVVRTSSLVEELGQIEYIFSDKTGTLTRNIMEFKSCSIAGHC
YIDKIPEDKTATVEDGIEVGYRKFDDLKKKLNDPSDEDSPIINDFLTLLA
TCHTVIPEFQSDGSIKYQAASPDEGALVQGGADLGYKFIIRKPNSVTVLL
EETGEEKEYQLLNICEFNSTRKRMSAIFRFPDGSIKLFCKGADTVILERL
DDEANQYVEATMRHLEDYASEGLRTLCLAMRDISEGEYEEWNSIYNEAAT
TLDNRAEKLDEAANLIEKNLILIGATAIEDKLQDGVPETIHTLQEAGIKI
WVLTGDRQETAINIGMSCRLLSEDMNLLIINEETRDDTERNLLEKINALN
EHQLSTHDMNTLALVIDGKSLGFALEPELEDYLLTVAKLCKAVICCRVSP
LQKALVVKMVKRKSSSLLLAIGDGANDVSMIQAAHVGVGISGMEGMQAAR
SADIAVGQFKFLKKLLLVHGSWSYQRISVAILYSFYKNTALYMTQFWYVF
ANAFSGQSIMESWTMSFYNLFFTVWPPFVIGVFDQFVSSRLLERYPQLYK
LGQKGQFFSVYIFWGWIINGFFHSAIVFIGTILIYRYGFALNMHGELADH
WSWGVTVYTTSVIIVLGKAALVTNQWTKFTLIAIPGSLLFWLIFFPIYAS
IFPHANISREYYGVVKHTYGSGVFWLTLIVLPIFALVRDFLWKYYKRMYE
PETYHVIQEMQKYNIS

Ligand information

• Ligand ID: ATP
• InChI: InChI=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
• InChIKey: ZKHQWZAMYRWXGA-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  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)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(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
• Formula: C10 H16 N5 O13 P3
• Name: ADENOSINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL14249
• DrugBank: DB00171
• ZINC: ZINC000004261765
• PDB chain: 7pem Chain A Residue 1403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7pem Substrate Transport and Specificity in a Phospholipid Flippase
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): D654 E655 F698 K703 R704 M705 K721 A723 L757 R838 R928
• Binding residue (residue number reindexed from 1): D473 E474 F517 K522 R523 M524 K540 A542 L576 R657 R747
• 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:0008289 lipid binding
• GO:0016887 ATP hydrolysis activity
• GO:0046872 metal ion binding
• GO:0070273 phosphatidylinositol-4-phosphate binding
• 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

Biological Process

• GO:0006892 post-Golgi vesicle-mediated transport
• GO:0006897 endocytosis
• GO:0015914 phospholipid transport
• GO:0032456 endocytic recycling
• GO:0045332 phospholipid translocation
• GO:0140331 aminophospholipid translocation

Cellular Component

• GO:0005768 endosome
• GO:0005783 endoplasmic reticulum
• GO:0005794 Golgi apparatus
• GO:0005802 trans-Golgi network
• GO:0005886 plasma membrane
• GO:0010008 endosome membrane
• GO:0016020 membrane
• GO:1990530 Cdc50p-Drs2p complex
• GO:1990531 phospholipid-translocating ATPase complex

External links

• PDB: RCSB:7pem, PDBe:7pem, PDBj:7pem
• PDBsum: 7pem
• UniProt: P39524|ATC3_YEAST Phospholipid-transporting ATPase DRS2 (Gene Name=DRS2)