Structure of PDB 6wm2 Chain R Binding Site BS05

Receptor Information

>6wm2 Chain R (length=753) Species: 9606 (Homo sapiens)

ELFRSEEMTLAQLFLQSEAAYCCVSELGELGKVQFRDLNPDVNVFQRKFV
NEVRRCEEMDRKLRFVEKEIRKANIPIMDTGENPEVPFPRDMIDLEANFE
KIENELKEINTNQEALKRNFLELTELKFILRKTGFVAGVINRERIPTFER
MLWRVCRGNVFLRQAEIENPLEDPVTGDYVHKSVFIIFFQGDQLKNRVKK
ICEGFRASLYPCPETPQERKEMASGVNTRIDDLQMVLNQTEDHRQRVLQA
AAKNIRVWFIKVRKMKAIYHTLNLCNIDVTQKCLIAEVWCPVTDLDSIQF
ALRRGTEHSGSTVPSILNRMQTNQTPPTYNKTNKFTYGFQNIVDAYGIGT
YREINPAPYTIITFPFLFAVMFGDFGHGILMTLFAVWMVLRESRILSQKN
ENEMFSTVFSGRYIILLMGVFSMYTGLIYNDCFSKSLNIFGSSWSVRPMF
TYNWTEETLRGNPVLQLNPALPGVFGGPYPFGIDPIWNIATNKLTFLNSF
KMKMSVILGIIHMLFGVSLSLFNHIYFKKPLNIYFGFIPEIIFMTSLFGY
LVILIFYKWTAYDAHTSENAPSLLIHFINMFLFSYPESGYSMLYSGQKGI
QCFLVVVALLCVPWMLLFKPLVLRRQYLRRKFDFGDTMVHQAIHTIEYCL
GCISNTASYLRLWALSLAHAQLSEVLWTMVIHIGLSVKSLAGGLVLFFFF
TAFATLTVAILLIMEGLSAFLHALRLHWVEFQNKFYSGTGFKFLPFSFEH
IRE

Ligand information

• Ligand ID: WJP
• InChI: InChI=1S/C26H48O7P2/c1-22(2)12-8-13-23(3)14-9-15-24(4)16-10-17-25(5)18-11-19-26(6)20-21-32-35(29,30)33-34(27,28)31-7/h12,14,16,18,26H,8-11,13,15,17,19-21H2,1-7H3,(H,27,28)(H,29,30)/b23-14+,24-16+,25-18-/t26-/m1/s1
• InChIKey: GDOCHZBDTMOKKR-FEJNUDJDSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: C[C@H](CC/C=C(/C)\CC/C=C(\C)/CC/C=C(\C)/CCC=C(C)C)CCOP(=O)(O)OP(=O)(O)OC
  CACTVS 3.385: CO[P](O)(=O)O[P](O)(=O)OCC[CH](C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C
  ACDLabs 12.01: CC(CC[C@H]=C(CC\C=C(/C)CC\C=C(\CC[C@H]=C(C)C)C)C)CCOP(=O)(O)OP(OC)(=O)O
  OpenEye OEToolkits 2.0.7: CC(CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C)CCOP(=O)(O)OP(=O)(O)OC
  CACTVS 3.385: CO[P](O)(=O)O[P](O)(=O)OCC[C@H](C)CC/C=C(/C)CC\C=C(/C)CC\C=C(/C)CCC=C(C)C
• Formula: C26 H48 O7 P2
• Name: methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate;
  dolichol-pp
• PDB chain: 6wm2 Chain R Residue 907

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6wm2 Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): K538 K593 L608 F616
• Binding residue (residue number reindexed from 1): K503 K558 L573 F581
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0046961 proton-transporting ATPase activity, rotational mechanism
• GO:0051117 ATPase binding

Biological Process

• GO:0007035 vacuolar acidification
• GO:0007042 lysosomal lumen acidification
• GO:0016241 regulation of macroautophagy
• GO:0048388 endosomal lumen acidification
• GO:0097401 synaptic vesicle lumen acidification
• GO:1902600 proton transmembrane transport

Cellular Component

• GO:0000220 vacuolar proton-transporting V-type ATPase, V0 domain
• GO:0005737 cytoplasm
• GO:0005765 lysosomal membrane
• GO:0005794 Golgi apparatus
• GO:0005829 cytosol
• GO:0005886 plasma membrane
• GO:0010008 endosome membrane
• GO:0016020 membrane
• GO:0016471 vacuolar proton-transporting V-type ATPase complex
• GO:0016607 nuclear speck
• GO:0030665 clathrin-coated vesicle membrane
• GO:0030667 secretory granule membrane
• GO:0030670 phagocytic vesicle membrane
• GO:0030672 synaptic vesicle membrane
• GO:0031410 cytoplasmic vesicle
• GO:0033176 proton-transporting V-type ATPase complex
• GO:0033179 proton-transporting V-type ATPase, V0 domain
• GO:0042470 melanosome
• GO:0043231 intracellular membrane-bounded organelle
• GO:0045202 synapse
• GO:0048471 perinuclear region of cytoplasm
• GO:0070062 extracellular exosome
• GO:0101003 ficolin-1-rich granule membrane

External links

• PDB: RCSB:6wm2, PDBe:6wm2, PDBj:6wm2
• PDBsum: 6wm2
• PubMed: 33065002
• UniProt: Q93050|VPP1_HUMAN V-type proton ATPase 116 kDa subunit a 1 (Gene Name=ATP6V0A1)