Structure of PDB 6lkn Chain A Binding Site BS01

Receptor Information

>6lkn Chain A (length=1064) Species: 9606 (Homo sapiens)

PVSETEAYIAQRFCDNRIVSSKYTLWNFLPKNLFEQFRRIANFYFLIIFL
VQVTVDTPTSPVTSGLPLFFVITVTAIKQGYEDWLRHRADNEVNKSTVYI
IENAKRVRKESEKIKVGDVVEVQADETFPCDLILLSSCTTDGTCYVTTAS
LDGESNCKTHYAVRDTIALCTAESIDTLRAAIECEQPQPDLYKFVGRINI
YSNSLEAVARSLGPENLLLKGATLKNTEKIYGVAVYTGMETKMALNYQGK
SQKRSAVEKSINAFLIVYLFILLTKAAVCTTLKYVWQSTPYNDEPWYNQK
TQKERETLKVLKMFTDFLSFMVLFNFIIPVSMYVTVEMQKFLGSFFISWD
KDFYDEEINEGALVNTSDLNEELGQVDYVFTDKTGTLTENSMEFIECCID
GHKYKGVTQEVDGLSQTDGTLTYFDKVDKNREELFLRALCLCHTVEIKTN
DAVDGATESAELTYISSSPDEIALVKGAKRYGFTFLGNRNGYMRVENQRK
EIEEYELLHTLNFDAVRRRMSVIVKTQEGDILLFCKGADSAVFPRVQNHE
IELTKVHVERNAMDGYRTLCVAFKEIAPDDYERINRQLIEAKMALQDREE
KMEKVFDDIETNMNLIGATAVEDKLQDQAAETIEALHAAGLKVWVLTGDK
METAKSTCYACRLFQTNTELLELTTKTIEESERKEDRLHELLIEYRKKLL
HEFPKSTRSFKKAWTEHQEYGLIIDGSTLSLILNSSQDSSSNNYKSIFLQ
ICMKCTAVLCCRMAPLQKAQIVRMVKNLKGSPITLSIGDGANDVSMILES
HVGIGIKGKEGRQAARNSDYSVPKFKHLKKLLLAHGHLYYVRIAHLVQYF
FYKNLCFILPQFLYQFFCGFSQQPLYDAAYLTMYNICFTSLPILAYSLLE
QHINIDTLTSDPRLYMKISGNAMLQLGPFLYWTFLAAFEGTVFFFGTYFL
FQTASLEENGKVYGNWTFGTIVFTVLVFTVTLKLALDTRFWTWINHFVIW
GSLAFYVFFSFFWGGIIWPFLKQQRMYFVFAQMLSSVSTWLAIILLIFIS
LFPEILLIVLKNVR

Ligand information

• Ligand ID: P5S
• InChI: InChI=1S/C42H82NO10P/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-40(44)50-35-38(36-51-54(48,49)52-37-39(43)42(46)47)53-41(45)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h38-39H,3-37,43H2,1-2H3,(H,46,47)(H,48,49)/t38-,39+/m1/s1
• InChIKey: TZCPCKNHXULUIY-RGULYWFUSA-N
• SMILES:
  CACTVS 3.370: CCCCCCCCCCCCCCCCCC(=O)OC[CH](CO[P](O)(=O)OC[CH](N)C(O)=O)OC(=O)CCCCCCCCCCCCCCCCC
  CACTVS 3.370: CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P](O)(=O)OC[C@H](N)C(O)=O)OC(=O)CCCCCCCCCCCCCCCCC
  ACDLabs 12.01: O=C(OC(COP(=O)(OCC(C(=O)O)N)O)COC(=O)CCCCCCCCCCCCCCCCC)CCCCCCCCCCCCCCCCC
  OpenEye OEToolkits 1.7.6: CCCCCCCCCCCCCCCCCC(=O)OCC(COP(=O)(O)OCC(C(=O)O)N)OC(=O)CCCCCCCCCCCCCCCCC
  OpenEye OEToolkits 1.7.6: CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OC[C@@H](C(=O)O)N)OC(=O)CCCCCCCCCCCCCCCCC
• Formula: C42 H82 N O10 P
• Name: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine;
  phosphatidyl serine
• ChEMBL: CHEMBL4297669
• DrugBank: DB00144
• ZINC: ZINC000085588270
• PDB chain: 6lkn Chain A Residue 1201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6lkn Crystal structure of a human plasma membrane phospholipid flippase.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): L93 P94
• Binding residue (residue number reindexed from 1): L66 P67
• Annotation score: 1

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

Biological Process

• GO:0006869 lipid transport
• GO:0015914 phospholipid transport
• GO:0034220 monoatomic ion transmembrane transport
• GO:0045332 phospholipid translocation
• GO:0140331 aminophospholipid translocation

Cellular Component

• GO:0005765 lysosomal membrane
• GO:0005768 endosome
• GO:0005783 endoplasmic reticulum
• GO:0005789 endoplasmic reticulum membrane
• GO:0005886 plasma membrane
• GO:0012505 endomembrane system
• GO:0016020 membrane
• GO:0031901 early endosome membrane
• GO:0055037 recycling endosome
• GO:0055038 recycling endosome membrane
• GO:1990531 phospholipid-translocating ATPase complex

External links

• PDB: RCSB:6lkn, PDBe:6lkn, PDBj:6lkn
• PDBsum: 6lkn
• PubMed: 32493773
• UniProt: Q8NB49|AT11C_HUMAN Phospholipid-transporting ATPase IG (Gene Name=ATP11C)