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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

3CF2

Structure of P97/vcp in complex with ADP/AMP-PNP

Replaces:  1YPW
Functional Information from GO Data
ChainGOidnamespacecontents
A0000153cellular_componentcytoplasmic ubiquitin ligase complex
A0000166molecular_functionnucleotide binding
A0000502cellular_componentproteasome complex
A0005515molecular_functionprotein binding
A0005524molecular_functionATP binding
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005737cellular_componentcytoplasm
A0005783cellular_componentendoplasmic reticulum
A0005789cellular_componentendoplasmic reticulum membrane
A0005811cellular_componentlipid droplet
A0005829cellular_componentcytosol
A0006281biological_processDNA repair
A0006302biological_processdouble-strand break repair
A0006511biological_processubiquitin-dependent protein catabolic process
A0006734biological_processobsolete NADH metabolic process
A0006888biological_processendoplasmic reticulum to Golgi vesicle-mediated transport
A0006914biological_processautophagy
A0006974biological_processDNA damage response
A0008289molecular_functionlipid binding
A0010494cellular_componentcytoplasmic stress granule
A0010498biological_processproteasomal protein catabolic process
A0010918biological_processpositive regulation of mitochondrial membrane potential
A0016236biological_processmacroautophagy
A0016567biological_processprotein ubiquitination
A0016787molecular_functionhydrolase activity
A0016887molecular_functionATP hydrolysis activity
A0019079biological_processviral genome replication
A0019903molecular_functionprotein phosphatase binding
A0019904molecular_functionprotein domain specific binding
A0019985biological_processtranslesion synthesis
A0030970biological_processretrograde protein transport, ER to cytosol
A0031334biological_processpositive regulation of protein-containing complex assembly
A0031593molecular_functionpolyubiquitin modification-dependent protein binding
A0031625molecular_functionubiquitin protein ligase binding
A0032436biological_processpositive regulation of proteasomal ubiquitin-dependent protein catabolic process
A0032510biological_processendosome to lysosome transport via multivesicular body sorting pathway
A0032991cellular_componentprotein-containing complex
A0034098cellular_componentVCP-NPL4-UFD1 AAA ATPase complex
A0034605biological_processcellular response to heat
A0035331biological_processnegative regulation of hippo signaling
A0035617biological_processstress granule disassembly
A0035800molecular_functiondeubiquitinase activator activity
A0035861cellular_componentsite of double-strand break
A0036064cellular_componentciliary basal body
A0036297biological_processinterstrand cross-link repair
A0036435molecular_functionK48-linked polyubiquitin modification-dependent protein binding
A0036503biological_processERAD pathway
A0036513cellular_componentDerlin-1 retrotranslocation complex
A0042288molecular_functionMHC class I protein binding
A0042802molecular_functionidentical protein binding
A0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
A0043209cellular_componentmyelin sheath
A0043531molecular_functionADP binding
A0044389molecular_functionubiquitin-like protein ligase binding
A0044877molecular_functionprotein-containing complex binding
A0045202cellular_componentsynapse
A0045732biological_processpositive regulation of protein catabolic process
A0045879biological_processnegative regulation of smoothened signaling pathway
A0046034biological_processATP metabolic process
A0048471cellular_componentperinuclear region of cytoplasm
A0050807biological_processregulation of synapse organization
A0051228biological_processmitotic spindle disassembly
A0061857biological_processendoplasmic reticulum stress-induced pre-emptive quality control
A0070842biological_processaggresome assembly
A0071218biological_processcellular response to misfolded protein
A0072389biological_processflavin adenine dinucleotide catabolic process
A0090263biological_processpositive regulation of canonical Wnt signaling pathway
A0097352biological_processautophagosome maturation
A0098978cellular_componentglutamatergic synapse
A0106300biological_processprotein-DNA covalent cross-linking repair
A0120186biological_processnegative regulation of protein localization to chromatin
A0140036molecular_functionubiquitin-modified protein reader activity
A0140455biological_processcytoplasm protein quality control
A1901224biological_processpositive regulation of non-canonical NF-kappaB signal transduction
A1903006biological_processpositive regulation of protein K63-linked deubiquitination
A1903715biological_processregulation of aerobic respiration
A1903843biological_processcellular response to arsenite ion
A1903862biological_processpositive regulation of oxidative phosphorylation
A1904288molecular_functionBAT3 complex binding
A1904949cellular_componentATPase complex
A1905634biological_processregulation of protein localization to chromatin
A1990381molecular_functionubiquitin-specific protease binding
A1990730cellular_componentVCP-NSFL1C complex
A2000060biological_processpositive regulation of ubiquitin-dependent protein catabolic process
A2001171biological_processpositive regulation of ATP biosynthetic process
B0000153cellular_componentcytoplasmic ubiquitin ligase complex
B0000166molecular_functionnucleotide binding
B0000502cellular_componentproteasome complex
B0005515molecular_functionprotein binding
B0005524molecular_functionATP binding
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0005737cellular_componentcytoplasm
B0005783cellular_componentendoplasmic reticulum
B0005789cellular_componentendoplasmic reticulum membrane
B0005811cellular_componentlipid droplet
B0005829cellular_componentcytosol
B0006281biological_processDNA repair
B0006302biological_processdouble-strand break repair
B0006511biological_processubiquitin-dependent protein catabolic process
B0006734biological_processobsolete NADH metabolic process
B0006888biological_processendoplasmic reticulum to Golgi vesicle-mediated transport
B0006914biological_processautophagy
B0006974biological_processDNA damage response
B0008289molecular_functionlipid binding
B0010494cellular_componentcytoplasmic stress granule
B0010498biological_processproteasomal protein catabolic process
B0010918biological_processpositive regulation of mitochondrial membrane potential
B0016236biological_processmacroautophagy
B0016567biological_processprotein ubiquitination
B0016787molecular_functionhydrolase activity
B0016887molecular_functionATP hydrolysis activity
B0019079biological_processviral genome replication
B0019903molecular_functionprotein phosphatase binding
B0019904molecular_functionprotein domain specific binding
B0019985biological_processtranslesion synthesis
B0030970biological_processretrograde protein transport, ER to cytosol
B0031334biological_processpositive regulation of protein-containing complex assembly
B0031593molecular_functionpolyubiquitin modification-dependent protein binding
B0031625molecular_functionubiquitin protein ligase binding
B0032436biological_processpositive regulation of proteasomal ubiquitin-dependent protein catabolic process
B0032510biological_processendosome to lysosome transport via multivesicular body sorting pathway
B0032991cellular_componentprotein-containing complex
B0034098cellular_componentVCP-NPL4-UFD1 AAA ATPase complex
B0034605biological_processcellular response to heat
B0035331biological_processnegative regulation of hippo signaling
B0035617biological_processstress granule disassembly
B0035800molecular_functiondeubiquitinase activator activity
B0035861cellular_componentsite of double-strand break
B0036064cellular_componentciliary basal body
B0036297biological_processinterstrand cross-link repair
B0036435molecular_functionK48-linked polyubiquitin modification-dependent protein binding
B0036503biological_processERAD pathway
B0036513cellular_componentDerlin-1 retrotranslocation complex
B0042288molecular_functionMHC class I protein binding
B0042802molecular_functionidentical protein binding
B0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
B0043209cellular_componentmyelin sheath
B0043531molecular_functionADP binding
B0044389molecular_functionubiquitin-like protein ligase binding
B0044877molecular_functionprotein-containing complex binding
B0045202cellular_componentsynapse
B0045732biological_processpositive regulation of protein catabolic process
B0045879biological_processnegative regulation of smoothened signaling pathway
B0046034biological_processATP metabolic process
B0048471cellular_componentperinuclear region of cytoplasm
B0050807biological_processregulation of synapse organization
B0051228biological_processmitotic spindle disassembly
B0061857biological_processendoplasmic reticulum stress-induced pre-emptive quality control
B0070842biological_processaggresome assembly
B0071218biological_processcellular response to misfolded protein
B0072389biological_processflavin adenine dinucleotide catabolic process
B0090263biological_processpositive regulation of canonical Wnt signaling pathway
B0097352biological_processautophagosome maturation
B0098978cellular_componentglutamatergic synapse
B0106300biological_processprotein-DNA covalent cross-linking repair
B0120186biological_processnegative regulation of protein localization to chromatin
B0140036molecular_functionubiquitin-modified protein reader activity
B0140455biological_processcytoplasm protein quality control
B1901224biological_processpositive regulation of non-canonical NF-kappaB signal transduction
B1903006biological_processpositive regulation of protein K63-linked deubiquitination
B1903715biological_processregulation of aerobic respiration
B1903843biological_processcellular response to arsenite ion
B1903862biological_processpositive regulation of oxidative phosphorylation
B1904288molecular_functionBAT3 complex binding
B1904949cellular_componentATPase complex
B1905634biological_processregulation of protein localization to chromatin
B1990381molecular_functionubiquitin-specific protease binding
B1990730cellular_componentVCP-NSFL1C complex
B2000060biological_processpositive regulation of ubiquitin-dependent protein catabolic process
B2001171biological_processpositive regulation of ATP biosynthetic process
C0000153cellular_componentcytoplasmic ubiquitin ligase complex
C0000166molecular_functionnucleotide binding
C0000502cellular_componentproteasome complex
C0005515molecular_functionprotein binding
C0005524molecular_functionATP binding
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005737cellular_componentcytoplasm
C0005783cellular_componentendoplasmic reticulum
C0005789cellular_componentendoplasmic reticulum membrane
C0005811cellular_componentlipid droplet
C0005829cellular_componentcytosol
C0006281biological_processDNA repair
C0006302biological_processdouble-strand break repair
C0006511biological_processubiquitin-dependent protein catabolic process
C0006734biological_processobsolete NADH metabolic process
C0006888biological_processendoplasmic reticulum to Golgi vesicle-mediated transport
C0006914biological_processautophagy
C0006974biological_processDNA damage response
C0008289molecular_functionlipid binding
C0010494cellular_componentcytoplasmic stress granule
C0010498biological_processproteasomal protein catabolic process
C0010918biological_processpositive regulation of mitochondrial membrane potential
C0016236biological_processmacroautophagy
C0016567biological_processprotein ubiquitination
C0016787molecular_functionhydrolase activity
C0016887molecular_functionATP hydrolysis activity
C0019079biological_processviral genome replication
C0019903molecular_functionprotein phosphatase binding
C0019904molecular_functionprotein domain specific binding
C0019985biological_processtranslesion synthesis
C0030970biological_processretrograde protein transport, ER to cytosol
C0031334biological_processpositive regulation of protein-containing complex assembly
C0031593molecular_functionpolyubiquitin modification-dependent protein binding
C0031625molecular_functionubiquitin protein ligase binding
C0032436biological_processpositive regulation of proteasomal ubiquitin-dependent protein catabolic process
C0032510biological_processendosome to lysosome transport via multivesicular body sorting pathway
C0032991cellular_componentprotein-containing complex
C0034098cellular_componentVCP-NPL4-UFD1 AAA ATPase complex
C0034605biological_processcellular response to heat
C0035331biological_processnegative regulation of hippo signaling
C0035617biological_processstress granule disassembly
C0035800molecular_functiondeubiquitinase activator activity
C0035861cellular_componentsite of double-strand break
C0036064cellular_componentciliary basal body
C0036297biological_processinterstrand cross-link repair
C0036435molecular_functionK48-linked polyubiquitin modification-dependent protein binding
C0036503biological_processERAD pathway
C0036513cellular_componentDerlin-1 retrotranslocation complex
C0042288molecular_functionMHC class I protein binding
C0042802molecular_functionidentical protein binding
C0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
C0043209cellular_componentmyelin sheath
C0043531molecular_functionADP binding
C0044389molecular_functionubiquitin-like protein ligase binding
C0044877molecular_functionprotein-containing complex binding
C0045202cellular_componentsynapse
C0045732biological_processpositive regulation of protein catabolic process
C0045879biological_processnegative regulation of smoothened signaling pathway
C0046034biological_processATP metabolic process
C0048471cellular_componentperinuclear region of cytoplasm
C0050807biological_processregulation of synapse organization
C0051228biological_processmitotic spindle disassembly
C0061857biological_processendoplasmic reticulum stress-induced pre-emptive quality control
C0070842biological_processaggresome assembly
C0071218biological_processcellular response to misfolded protein
C0072389biological_processflavin adenine dinucleotide catabolic process
C0090263biological_processpositive regulation of canonical Wnt signaling pathway
C0097352biological_processautophagosome maturation
C0098978cellular_componentglutamatergic synapse
C0106300biological_processprotein-DNA covalent cross-linking repair
C0120186biological_processnegative regulation of protein localization to chromatin
C0140036molecular_functionubiquitin-modified protein reader activity
C0140455biological_processcytoplasm protein quality control
C1901224biological_processpositive regulation of non-canonical NF-kappaB signal transduction
C1903006biological_processpositive regulation of protein K63-linked deubiquitination
C1903715biological_processregulation of aerobic respiration
C1903843biological_processcellular response to arsenite ion
C1903862biological_processpositive regulation of oxidative phosphorylation
C1904288molecular_functionBAT3 complex binding
C1904949cellular_componentATPase complex
C1905634biological_processregulation of protein localization to chromatin
C1990381molecular_functionubiquitin-specific protease binding
C1990730cellular_componentVCP-NSFL1C complex
C2000060biological_processpositive regulation of ubiquitin-dependent protein catabolic process
C2001171biological_processpositive regulation of ATP biosynthetic process
D0000153cellular_componentcytoplasmic ubiquitin ligase complex
D0000166molecular_functionnucleotide binding
D0000502cellular_componentproteasome complex
D0005515molecular_functionprotein binding
D0005524molecular_functionATP binding
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0005737cellular_componentcytoplasm
D0005783cellular_componentendoplasmic reticulum
D0005789cellular_componentendoplasmic reticulum membrane
D0005811cellular_componentlipid droplet
D0005829cellular_componentcytosol
D0006281biological_processDNA repair
D0006302biological_processdouble-strand break repair
D0006511biological_processubiquitin-dependent protein catabolic process
D0006734biological_processobsolete NADH metabolic process
D0006888biological_processendoplasmic reticulum to Golgi vesicle-mediated transport
D0006914biological_processautophagy
D0006974biological_processDNA damage response
D0008289molecular_functionlipid binding
D0010494cellular_componentcytoplasmic stress granule
D0010498biological_processproteasomal protein catabolic process
D0010918biological_processpositive regulation of mitochondrial membrane potential
D0016236biological_processmacroautophagy
D0016567biological_processprotein ubiquitination
D0016787molecular_functionhydrolase activity
D0016887molecular_functionATP hydrolysis activity
D0019079biological_processviral genome replication
D0019903molecular_functionprotein phosphatase binding
D0019904molecular_functionprotein domain specific binding
D0019985biological_processtranslesion synthesis
D0030970biological_processretrograde protein transport, ER to cytosol
D0031334biological_processpositive regulation of protein-containing complex assembly
D0031593molecular_functionpolyubiquitin modification-dependent protein binding
D0031625molecular_functionubiquitin protein ligase binding
D0032436biological_processpositive regulation of proteasomal ubiquitin-dependent protein catabolic process
D0032510biological_processendosome to lysosome transport via multivesicular body sorting pathway
D0032991cellular_componentprotein-containing complex
D0034098cellular_componentVCP-NPL4-UFD1 AAA ATPase complex
D0034605biological_processcellular response to heat
D0035331biological_processnegative regulation of hippo signaling
D0035617biological_processstress granule disassembly
D0035800molecular_functiondeubiquitinase activator activity
D0035861cellular_componentsite of double-strand break
D0036064cellular_componentciliary basal body
D0036297biological_processinterstrand cross-link repair
D0036435molecular_functionK48-linked polyubiquitin modification-dependent protein binding
D0036503biological_processERAD pathway
D0036513cellular_componentDerlin-1 retrotranslocation complex
D0042288molecular_functionMHC class I protein binding
D0042802molecular_functionidentical protein binding
D0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
D0043209cellular_componentmyelin sheath
D0043531molecular_functionADP binding
D0044389molecular_functionubiquitin-like protein ligase binding
D0044877molecular_functionprotein-containing complex binding
D0045202cellular_componentsynapse
D0045732biological_processpositive regulation of protein catabolic process
D0045879biological_processnegative regulation of smoothened signaling pathway
D0046034biological_processATP metabolic process
D0048471cellular_componentperinuclear region of cytoplasm
D0050807biological_processregulation of synapse organization
D0051228biological_processmitotic spindle disassembly
D0061857biological_processendoplasmic reticulum stress-induced pre-emptive quality control
D0070842biological_processaggresome assembly
D0071218biological_processcellular response to misfolded protein
D0072389biological_processflavin adenine dinucleotide catabolic process
D0090263biological_processpositive regulation of canonical Wnt signaling pathway
D0097352biological_processautophagosome maturation
D0098978cellular_componentglutamatergic synapse
D0106300biological_processprotein-DNA covalent cross-linking repair
D0120186biological_processnegative regulation of protein localization to chromatin
D0140036molecular_functionubiquitin-modified protein reader activity
D0140455biological_processcytoplasm protein quality control
D1901224biological_processpositive regulation of non-canonical NF-kappaB signal transduction
D1903006biological_processpositive regulation of protein K63-linked deubiquitination
D1903715biological_processregulation of aerobic respiration
D1903843biological_processcellular response to arsenite ion
D1903862biological_processpositive regulation of oxidative phosphorylation
D1904288molecular_functionBAT3 complex binding
D1904949cellular_componentATPase complex
D1905634biological_processregulation of protein localization to chromatin
D1990381molecular_functionubiquitin-specific protease binding
D1990730cellular_componentVCP-NSFL1C complex
D2000060biological_processpositive regulation of ubiquitin-dependent protein catabolic process
D2001171biological_processpositive regulation of ATP biosynthetic process
Functional Information from PDB Data
site_idAC1
Number of Residues13
DetailsBINDING SITE FOR RESIDUE ADP A 807
ChainResidue
AASP205
AHIS384
AGLY408
AALA409
BARG359
AGLY207
AGLY248
ATHR249
AGLY250
ALYS251
ATHR252
ALEU253
AILE380
site_idAC2
Number of Residues15
DetailsBINDING SITE FOR RESIDUE ANP A 901
ChainResidue
AASP478
AILE479
APRO519
APRO520
AGLY521
ACYS522
AGLY523
ALYS524
ATHR525
ALEU526
AASP577
AASN624
AILE656
ATHR688
BARG635
site_idAC3
Number of Residues14
DetailsBINDING SITE FOR RESIDUE ADP B 807
ChainResidue
ALYS236
AARG359
BASP205
BGLY207
BGLY248
BTHR249
BGLY250
BLYS251
BTHR252
BLEU253
BILE380
BHIS384
BGLY408
BALA409
site_idAC4
Number of Residues15
DetailsBINDING SITE FOR RESIDUE ANP B 901
ChainResidue
AARG635
BASP478
BILE479
BPRO519
BPRO520
BGLY521
BCYS522
BGLY523
BLYS524
BTHR525
BLEU526
BASP577
BASN624
BILE656
BTHR688
site_idAC5
Number of Residues14
DetailsBINDING SITE FOR RESIDUE ADP C 807
ChainResidue
CASP205
CGLY207
CGLY248
CTHR249
CGLY250
CLYS251
CTHR252
CLEU253
CILE380
CHIS384
CGLY408
CALA409
DLYS236
DARG359
site_idAC6
Number of Residues15
DetailsBINDING SITE FOR RESIDUE ANP C 901
ChainResidue
CASP478
CILE479
CPRO519
CPRO520
CGLY521
CCYS522
CGLY523
CLYS524
CTHR525
CLEU526
CASP577
CASN624
CILE656
CTHR688
DARG635
site_idAC7
Number of Residues14
DetailsBINDING SITE FOR RESIDUE ADP D 807
ChainResidue
DALA409
CLYS236
CARG359
DASP205
DGLY207
DGLY248
DTHR249
DGLY250
DLYS251
DTHR252
DLEU253
DILE380
DHIS384
DGLY408
site_idAC8
Number of Residues15
DetailsBINDING SITE FOR RESIDUE ANP D 901
ChainResidue
CARG635
DASP478
DILE479
DPRO519
DPRO520
DGLY521
DCYS522
DGLY523
DLYS524
DTHR525
DLEU526
DASP577
DASN624
DILE656
DTHR688
Functional Information from PROSITE/UniProt
site_idPS00674
Number of Residues19
DetailsAAA AAA-protein family signature. ViVMaATNrpnsIDpALr.R
ChainResidueDetails
AVAL341-ARG359
AVAL617-ARG635
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues48
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"11163219","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"14988733","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"P55072","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues12
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P55072","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues4
DetailsModified residue: {"description":"N6,N6,N6-trimethyllysine; by VCPKMT","evidences":[{"source":"PubMed","id":"22948820","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues4
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P55072","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues8
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"23806337","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues4
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"23806337","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

239149

PDB entries from 2025-07-23

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