Structure of PDB 6wm3 Chain B

Receptor sequence
>6wm3B (length=600) Species: 9606 (Homo sapiens) [Search protein sequence]
TFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEIIRLEGDMATIQV
YEETSGVSVGDPVLRTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSI
YIPRGVNVSALSRDIKWDFTPCKNLRVGSHITGGDIYGIVSENSLIKHKI
MLPPRNRGTVTYIAPPGNYDTSDVVLELEFEGVKEKFTMVQVWPVRQVRP
VTEKLPANHPLLTGQRVLDALFPCVQGGTTAIPGAFGCGKTVISQSLSKY
SNSDVIIYVGCGERGNEMSEVLRDFPELTMEVDGKVESIMKRTALVANTS
NMPVAAREASIYTGITLSEYFRDMGYHVSMMADSTSRWAEALREISGRLA
EMPADSGYPAYLGARLASFYERAGRVKCLGNPEREGSVSIVGAVSPPGGD
FSDPVTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMRALDEYYD
KHFTEFVPLRTKAKEILQEEEDLAEIVQLVGKASLAETDKITLEVAKLIK
DDFLQQNGYTPYDRFCPFYKTVGMLSNMIAFYDMARRAVETTAQSDNKIT
WSIIREHMGDILYKLSSMKFKDPLKDGEAKIKSDYAQLLEDMQNAFRSLE
3D structure
PDB6wm3 Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly.
ChainB
Resolution3.4 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) K256 E279 R280 K456
Catalytic site (residue number reindexed from 1) K240 E263 R264 K440
Enzyme Commision number 7.1.2.2: H(+)-transporting two-sector ATPase.
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 ADP B G253 G255 K256 T257 V258 F445 G524 Y525 G237 G239 K240 T241 V242 F429 G508 Y509
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism
GO:0046961 proton-transporting ATPase activity, rotational mechanism
Biological Process
GO:0006879 intracellular iron ion homeostasis
GO:0007035 vacuolar acidification
GO:0007042 lysosomal lumen acidification
GO:0015986 proton motive force-driven ATP synthesis
GO:0016241 regulation of macroautophagy
GO:0036295 cellular response to increased oxygen levels
GO:0046034 ATP metabolic process
GO:0048388 endosomal lumen acidification
GO:0051452 intracellular pH reduction
GO:0061795 Golgi lumen acidification
GO:0097401 synaptic vesicle lumen acidification
GO:1902600 proton transmembrane transport
Cellular Component
GO:0000139 Golgi membrane
GO:0000221 vacuolar proton-transporting V-type ATPase, V1 domain
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005902 microvillus
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0016324 apical plasma membrane
GO:0016469 proton-transporting two-sector ATPase complex
GO:0030133 transport vesicle
GO:0030141 secretory granule
GO:0030665 clathrin-coated vesicle membrane
GO:0031090 organelle membrane
GO:0031410 cytoplasmic vesicle
GO:0033176 proton-transporting V-type ATPase complex
GO:0033180 proton-transporting V-type ATPase, V1 domain
GO:0043231 intracellular membrane-bounded organelle
GO:0070062 extracellular exosome
GO:0098850 extrinsic component of synaptic vesicle membrane
GO:1904949 ATPase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6wm3, PDBe:6wm3, PDBj:6wm3
PDBsum6wm3
PubMed33065002
UniProtP38606|VATA_HUMAN V-type proton ATPase catalytic subunit A (Gene Name=ATP6V1A)

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