Structure of PDB 9brd Chain a

Receptor sequence
>9brda (length=770) Species: 10116 (Rattus norvegicus) [Search protein sequence]
ELFRSEEMTLAQLFLQSEAAYCCVSELEELGKVQFRDLNPDVNVFQRKFV
NEVRRCEEMDRKLRFVEKEIRKANIPIMDTGENPEVPFPRDMIDLEANFE
KIENELKEINTNQEALKRNFLELTELKFILRKTQQFFDEMADPDLLRLGF
VAGVINRERIPTFERMLWRVCRGNVFLRQAEIENPLEDPVTGDYVHKSVF
IIFFQGDQLKNRVKKICEGFRASLYPCPETPQERKEMASGVNTRIDDLQM
VLNQTEDHRQRVLQAAAKNIRVWFIKVRKMKAIYHTLNLCNIDVTQKCLI
AEVWCPVTDLDSIQFALRRGTEHSGSTVPSILNRMQTNQTPPTYNKTNKF
THGFQNIVDAYGIGTYREINPAPYTVITFPFLFAVMFGDFGHGILMTLFA
VWMVLRESRILSQKNENEMFSMVFSGRYIILLMGLFSIYTGLIYNDCFSK
SLNIFGSSWSVRPMFTIGNWTEETLLGSSVLQLNPAIPGVFGGPYPFGID
PIWNIATNKLTFLNSFKMKMSVILGIIHMLFGVSLSLFNHIYFKKPLNIY
FGFIPEIIFMSSLFGYLVILIFYKWTAYDAHSSRNAPSLLIHFINMFLFS
YPESGNAMLYSGQKGIQCFLIVVAMLCVPWMLLFKPLILRHQYLRKKHVF
DFGDTMVHQAIHTIEYCLGCISNTASYLRLWALSLAHAQLSEVLWTMVIH
IGLHVRSLAGGLGLFFIFAAFATLTVAILLIMEGLSAFLHALRLHWVEFQ
NKFYTGTGFKFLPFSFEHIR
3D structure
PDB9brd High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles.
Chaina
Resolution3.5 Å
3D
structure
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Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 BMA a S603 R604 S583 R584
BS02 MAN a Q502 L503 N504 Q482 L483 N484
BS03 GLC a W490 S498 W470 S478
BS04 GLC a E493 T494 E473 T474
BS05 WJP a S535 K539 S608 L609 L610 I733 S515 K519 S588 L589 L590 I671
BS06 LP3 a L415 C467 F468 K470 S471 L472 L395 C447 F448 K450 S451 L452
Gene Ontology
Biological Process
GO:0007035 vacuolar acidification
GO:0008150 biological_process
GO:0016241 regulation of macroautophagy
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:0005886 plasma membrane
GO:0016020 membrane
GO:0016471 vacuolar proton-transporting V-type ATPase complex
GO:0030665 clathrin-coated vesicle membrane
GO:0030672 synaptic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0042470 melanosome
GO:0043195 terminal bouton
GO:0045202 synapse
GO:0048471 perinuclear region of cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:9brd, PDBe:9brd, PDBj:9brd
PDBsum9brd
PubMed38900912
UniProtP25286|VPP1_RAT V-type proton ATPase 116 kDa subunit a 1 (Gene Name=Atp6v0a1)

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