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7Z1X

Crystal structure of human Gasdermin D complexed with nanobodies VHH-2 and VHH-6

Functional Information from GO Data
ChainGOidnamespacecontents
A0001786molecular_functionphosphatidylserine binding
A0005515molecular_functionprotein binding
A0005546molecular_functionphosphatidylinositol-4,5-bisphosphate binding
A0005576cellular_componentextracellular region
A0005615cellular_componentextracellular space
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0005829cellular_componentcytosol
A0005886cellular_componentplasma membrane
A0006954biological_processinflammatory response
A0008289molecular_functionlipid binding
A0009306biological_processprotein secretion
A0012501biological_processprogrammed cell death
A0016020cellular_componentmembrane
A0022829molecular_functionwide pore channel activity
A0031668biological_processobsolete cellular response to extracellular stimulus
A0031966cellular_componentmitochondrial membrane
A0032731biological_processpositive regulation of interleukin-1 beta production
A0035580cellular_componentspecific granule lumen
A0042742biological_processdefense response to bacterium
A0045087biological_processinnate immune response
A0046931biological_processpore complex assembly
A0050729biological_processpositive regulation of inflammatory response
A0050829biological_processdefense response to Gram-negative bacterium
A0050830biological_processdefense response to Gram-positive bacterium
A0051260biological_processprotein homooligomerization
A0055085biological_processtransmembrane transport
A0061702cellular_componentcanonical inflammasome complex
A0070269biological_processpyroptotic inflammatory response
A0070273molecular_functionphosphatidylinositol-4-phosphate binding
A0070300molecular_functionphosphatidic acid binding
A0072559cellular_componentNLRP3 inflammasome complex
A0141201biological_processpyroptotic cell death
A1901612molecular_functioncardiolipin binding
A1904724cellular_componenttertiary granule lumen
A1904813cellular_componentficolin-1-rich granule lumen
D0001786molecular_functionphosphatidylserine binding
D0005515molecular_functionprotein binding
D0005546molecular_functionphosphatidylinositol-4,5-bisphosphate binding
D0005576cellular_componentextracellular region
D0005615cellular_componentextracellular space
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0005737cellular_componentcytoplasm
D0005739cellular_componentmitochondrion
D0005829cellular_componentcytosol
D0005886cellular_componentplasma membrane
D0006954biological_processinflammatory response
D0008289molecular_functionlipid binding
D0009306biological_processprotein secretion
D0012501biological_processprogrammed cell death
D0016020cellular_componentmembrane
D0022829molecular_functionwide pore channel activity
D0031668biological_processobsolete cellular response to extracellular stimulus
D0031966cellular_componentmitochondrial membrane
D0032731biological_processpositive regulation of interleukin-1 beta production
D0035580cellular_componentspecific granule lumen
D0042742biological_processdefense response to bacterium
D0045087biological_processinnate immune response
D0046931biological_processpore complex assembly
D0050729biological_processpositive regulation of inflammatory response
D0050829biological_processdefense response to Gram-negative bacterium
D0050830biological_processdefense response to Gram-positive bacterium
D0051260biological_processprotein homooligomerization
D0055085biological_processtransmembrane transport
D0061702cellular_componentcanonical inflammasome complex
D0070269biological_processpyroptotic inflammatory response
D0070273molecular_functionphosphatidylinositol-4-phosphate binding
D0070300molecular_functionphosphatidic acid binding
D0072559cellular_componentNLRP3 inflammasome complex
D0141201biological_processpyroptotic cell death
D1901612molecular_functioncardiolipin binding
D1904724cellular_componenttertiary granule lumen
D1904813cellular_componentficolin-1-rich granule lumen
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues46
DetailsTRANSMEM: Beta stranded => ECO:0000269|PubMed:33883744, ECO:0007744|PDB:6VFE
ChainResidueDetails
AGLN91-ALA97
ALYS103-ALA108
AGLY191-GLN197
AGLN202-ILE208
DGLN91-ALA97
DLYS103-ALA108
DGLY191-GLN197
DGLN202-ILE208

site_idSWS_FT_FI2
Number of Residues2
DetailsSITE: Cleavage; by CASP3 or CASP7 => ECO:0000269|PubMed:28045099, ECO:0000269|PubMed:28392147, ECO:0000269|PubMed:37327784
ChainResidueDetails
AASP87
DASP87

site_idSWS_FT_FI3
Number of Residues2
DetailsSITE: Cleavage; by enterovirus 71 (EV71) Protease 3C and coronavirus SARS-CoV-2 proteinase nsp5 => ECO:0000269|PubMed:28679757, ECO:0000269|PubMed:35594856
ChainResidueDetails
ALYS204
DLYS204

site_idSWS_FT_FI4
Number of Residues2
DetailsSITE: Cleavage; by caspases CASP1, CASP4, CASP5 and CASP8 => ECO:0000269|PubMed:26375003, ECO:0000269|PubMed:32109412, ECO:0000305|PubMed:29898893
ChainResidueDetails
ALEU312
DLEU312

site_idSWS_FT_FI5
Number of Residues2
DetailsSITE: Cleavage; by papain => ECO:0000269|PubMed:35794369
ChainResidueDetails
AARG327
DARG327

site_idSWS_FT_FI6
Number of Residues4
DetailsMOD_RES: Phosphotyrosine => ECO:0007744|PubMed:15592455
ChainResidueDetails
ATYR37
ATYR158
DTYR37
DTYR158

site_idSWS_FT_FI7
Number of Residues10
DetailsMOD_RES: S-(2-succinyl)cysteine => ECO:0000269|PubMed:32820063
ChainResidueDetails
ACYS56
AGLN202
AASP305
AASP346
DCYS56
DGLN202
DASP305
DASP346

site_idSWS_FT_FI8
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569
ChainResidueDetails
AGLY196
DGLY196

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PDB entries from 2024-07-24

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