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6NQ2

Cryo-EM structure of human TPC2 channel in the ligand-bound closed state

Functional Information from GO Data
ChainGOidnamespacecontents
A0005216molecular_functionmonoatomic ion channel activity
A0005245molecular_functionvoltage-gated calcium channel activity
A0005248molecular_functionvoltage-gated sodium channel activity
A0005262molecular_functioncalcium channel activity
A0005515molecular_functionprotein binding
A0005764cellular_componentlysosome
A0005765cellular_componentlysosomal membrane
A0005768cellular_componentendosome
A0005829cellular_componentcytosol
A0006811biological_processmonoatomic ion transport
A0006874biological_processintracellular calcium ion homeostasis
A0006939biological_processsmooth muscle contraction
A0007040biological_processlysosome organization
A0010008cellular_componentendosome membrane
A0010506biological_processregulation of autophagy
A0015280molecular_functionligand-gated sodium channel activity
A0016020cellular_componentmembrane
A0017157biological_processregulation of exocytosis
A0019065biological_processreceptor-mediated endocytosis of virus by host cell
A0019722biological_processcalcium-mediated signaling
A0019901molecular_functionprotein kinase binding
A0022832molecular_functionvoltage-gated channel activity
A0031902cellular_componentlate endosome membrane
A0033162cellular_componentmelanosome membrane
A0033280biological_processresponse to vitamin D
A0034220biological_processmonoatomic ion transmembrane transport
A0034702cellular_componentmonoatomic ion channel complex
A0035725biological_processsodium ion transmembrane transport
A0036020cellular_componentendolysosome membrane
A0042802molecular_functionidentical protein binding
A0048086biological_processnegative regulation of developmental pigmentation
A0051209biological_processrelease of sequestered calcium ion into cytosol
A0051452biological_processintracellular pH reduction
A0055085biological_processtransmembrane transport
A0070588biological_processcalcium ion transmembrane transport
A0072345molecular_functionNAADP-sensitive calcium-release channel activity
A0075509biological_processendocytosis involved in viral entry into host cell
A0080025molecular_functionphosphatidylinositol-3,5-bisphosphate binding
A0090117biological_processendosome to lysosome transport of low-density lipoprotein particle
A0097682molecular_functionintracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity
B0005216molecular_functionmonoatomic ion channel activity
B0005245molecular_functionvoltage-gated calcium channel activity
B0005248molecular_functionvoltage-gated sodium channel activity
B0005262molecular_functioncalcium channel activity
B0005515molecular_functionprotein binding
B0005764cellular_componentlysosome
B0005765cellular_componentlysosomal membrane
B0005768cellular_componentendosome
B0005829cellular_componentcytosol
B0006811biological_processmonoatomic ion transport
B0006874biological_processintracellular calcium ion homeostasis
B0006939biological_processsmooth muscle contraction
B0007040biological_processlysosome organization
B0010008cellular_componentendosome membrane
B0010506biological_processregulation of autophagy
B0015280molecular_functionligand-gated sodium channel activity
B0016020cellular_componentmembrane
B0017157biological_processregulation of exocytosis
B0019065biological_processreceptor-mediated endocytosis of virus by host cell
B0019722biological_processcalcium-mediated signaling
B0019901molecular_functionprotein kinase binding
B0022832molecular_functionvoltage-gated channel activity
B0031902cellular_componentlate endosome membrane
B0033162cellular_componentmelanosome membrane
B0033280biological_processresponse to vitamin D
B0034220biological_processmonoatomic ion transmembrane transport
B0034702cellular_componentmonoatomic ion channel complex
B0035725biological_processsodium ion transmembrane transport
B0036020cellular_componentendolysosome membrane
B0042802molecular_functionidentical protein binding
B0048086biological_processnegative regulation of developmental pigmentation
B0051209biological_processrelease of sequestered calcium ion into cytosol
B0051452biological_processintracellular pH reduction
B0055085biological_processtransmembrane transport
B0070588biological_processcalcium ion transmembrane transport
B0072345molecular_functionNAADP-sensitive calcium-release channel activity
B0075509biological_processendocytosis involved in viral entry into host cell
B0080025molecular_functionphosphatidylinositol-3,5-bisphosphate binding
B0090117biological_processendosome to lysosome transport of low-density lipoprotein particle
B0097682molecular_functionintracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity
Functional Information from PDB Data
site_idAC1
Number of Residues6
Detailsbinding site for residue EUJ A 1000
ChainResidue
ATRP157
ASER200
ALYS204
ALYS207
AARG210
AARG329

site_idAC2
Number of Residues6
Detailsbinding site for residue EUJ B 1000
ChainResidue
BLYS207
BARG210
BARG329
BTRP157
BSER200
BLYS204

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues606
DetailsTOPO_DOM: Cytoplasmic => ECO:0000255
ChainResidueDetails
AMET1-ARG84
BTHR205-SER218
BILE311-TYR436
BLYS487-ASN502
BVAL576-ARG580
BGLU695-ARG752
ATRP149-ASN155
ATHR205-SER218
AILE311-TYR436
ALYS487-ASN502
AVAL576-ARG580
AGLU695-ARG752
BMET1-ARG84
BTRP149-ASN155

site_idSWS_FT_FI2
Number of Residues40
DetailsTRANSMEM: Helical; Name=S1 of repeat I => ECO:0000255
ChainResidueDetails
ATHR85-LEU105
BTHR85-LEU105

site_idSWS_FT_FI3
Number of Residues264
DetailsTOPO_DOM: Extracellular => ECO:0000255
ChainResidueDetails
ATHR106-SER127
BSER177-PRO183
BGLY240-TYR254
BPRO280-ALA289
BLEU460-ASP465
BARG524-ARG554
BARG602-ASN635
BLEU659-TYR673
ASER177-PRO183
AGLY240-TYR254
APRO280-ALA289
ALEU460-ASP465
AARG524-ARG554
AARG602-ASN635
ALEU659-TYR673
BTHR106-SER127

site_idSWS_FT_FI4
Number of Residues40
DetailsTRANSMEM: Helical; Name=S2 of repeat I => ECO:0000255
ChainResidueDetails
AVAL128-GLY148
BVAL128-GLY148

site_idSWS_FT_FI5
Number of Residues40
DetailsTRANSMEM: Helical; Name=S3 of repeat I => ECO:0000255
ChainResidueDetails
ALEU156-LEU176
BLEU156-LEU176

site_idSWS_FT_FI6
Number of Residues40
DetailsTRANSMEM: Helical; Name=S4 of repeat I => ECO:0000255
ChainResidueDetails
ALEU184-LYS204
BLEU184-LYS204

site_idSWS_FT_FI7
Number of Residues40
DetailsTRANSMEM: Helical; Name=S5 of repeat I => ECO:0000255
ChainResidueDetails
AVAL219-ALA239
BVAL219-ALA239

site_idSWS_FT_FI8
Number of Residues92
DetailsINTRAMEM: Helical; Pore-forming => ECO:0000255
ChainResidueDetails
APHE255-ILE279
APHE636-PHE658
BPHE255-ILE279
BPHE636-PHE658

site_idSWS_FT_FI9
Number of Residues40
DetailsTRANSMEM: Helical; Name=S6 of repeat I => ECO:0000255
ChainResidueDetails
AILE290-ILE310
BILE290-ILE310

site_idSWS_FT_FI10
Number of Residues44
DetailsTRANSMEM: Helical; Name=S1 of repeat II => ECO:0000255
ChainResidueDetails
ALEU437-VAL459
BLEU437-VAL459

site_idSWS_FT_FI11
Number of Residues40
DetailsTRANSMEM: Helical; Name=S2 of repeat II => ECO:0000255
ChainResidueDetails
AASP466-LEU486
BASP466-LEU486

site_idSWS_FT_FI12
Number of Residues40
DetailsTRANSMEM: Helical; Name=S3 of repeat II => ECO:0000255
ChainResidueDetails
AVAL503-TYR523
BVAL503-TYR523

site_idSWS_FT_FI13
Number of Residues40
DetailsTRANSMEM: Helical; Name=S4 of repeat II => ECO:0000255
ChainResidueDetails
APHE555-LEU575
BPHE555-LEU575

site_idSWS_FT_FI14
Number of Residues40
DetailsTRANSMEM: Helical; Name=S5 of repeat II => ECO:0000255
ChainResidueDetails
AALA581-PHE601
BALA581-PHE601

site_idSWS_FT_FI15
Number of Residues40
DetailsTRANSMEM: Helical; Name=S6 of repeat II => ECO:0000255
ChainResidueDetails
APHE674-LEU694
BPHE674-LEU694

site_idSWS_FT_FI16
Number of Residues4
DetailsCARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000255
ChainResidueDetails
AASN611
AASN618
BASN611
BASN618

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PDB entries from 2024-11-06

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