3CF1

Structure of P97/vcp in complex with ADP/ADP.alfx

Replaces:  1OZ4Replaces:  1YQ0

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000153	cellular_component	cytoplasmic ubiquitin ligase complex
A	0000166	molecular_function	nucleotide binding
A	0000502	cellular_component	proteasome complex
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005783	cellular_component	endoplasmic reticulum
A	0005789	cellular_component	endoplasmic reticulum membrane
A	0005811	cellular_component	lipid droplet
A	0005829	cellular_component	cytosol
A	0006281	biological_process	DNA repair
A	0006302	biological_process	double-strand break repair
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0006888	biological_process	endoplasmic reticulum to Golgi vesicle-mediated transport
A	0006914	biological_process	autophagy
A	0006974	biological_process	DNA damage response
A	0007249	biological_process	canonical NF-kappaB signal transduction
A	0008289	molecular_function	lipid binding
A	0010494	cellular_component	cytoplasmic stress granule
A	0010498	biological_process	proteasomal protein catabolic process
A	0010918	biological_process	positive regulation of mitochondrial membrane potential
A	0016236	biological_process	macroautophagy
A	0016567	biological_process	protein ubiquitination
A	0016787	molecular_function	hydrolase activity
A	0016887	molecular_function	ATP hydrolysis activity
A	0019079	biological_process	viral genome replication
A	0019674	biological_process	NAD+ metabolic process
A	0019903	molecular_function	protein phosphatase binding
A	0019904	molecular_function	protein domain specific binding
A	0019985	biological_process	translesion synthesis
A	0030970	biological_process	retrograde protein transport, ER to cytosol
A	0031334	biological_process	positive regulation of protein-containing complex assembly
A	0031593	molecular_function	polyubiquitin modification-dependent protein binding
A	0031625	molecular_function	ubiquitin protein ligase binding
A	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
A	0032510	biological_process	endosome to lysosome transport via multivesicular body sorting pathway
A	0032991	cellular_component	protein-containing complex
A	0034098	cellular_component	VCP-NPL4-UFD1 AAA ATPase complex
A	0034605	biological_process	cellular response to heat
A	0035331	biological_process	negative regulation of hippo signaling
A	0035617	biological_process	stress granule disassembly
A	0035800	molecular_function	deubiquitinase activator activity
A	0035861	cellular_component	site of double-strand break
A	0036064	cellular_component	ciliary basal body
A	0036297	biological_process	interstrand cross-link repair
A	0036435	molecular_function	K48-linked polyubiquitin modification-dependent protein binding
A	0036503	biological_process	ERAD pathway
A	0036513	cellular_component	Derlin-1 retrotranslocation complex
A	0042288	molecular_function	MHC class I protein binding
A	0042802	molecular_function	identical protein binding
A	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
A	0043209	cellular_component	myelin sheath
A	0043531	molecular_function	ADP binding
A	0044389	molecular_function	ubiquitin-like protein ligase binding
A	0044877	molecular_function	protein-containing complex binding
A	0045202	cellular_component	synapse
A	0045732	biological_process	positive regulation of protein catabolic process
A	0045879	biological_process	negative regulation of smoothened signaling pathway
A	0046034	biological_process	ATP metabolic process
A	0048471	cellular_component	perinuclear region of cytoplasm
A	0050807	biological_process	regulation of synapse organization
A	0051228	biological_process	mitotic spindle disassembly
A	0061857	biological_process	endoplasmic reticulum stress-induced pre-emptive quality control
A	0070842	biological_process	aggresome assembly
A	0071218	biological_process	cellular response to misfolded protein
A	0072389	biological_process	flavin adenine dinucleotide catabolic process
A	0090263	biological_process	positive regulation of canonical Wnt signaling pathway
A	0097352	biological_process	autophagosome maturation
A	0098978	cellular_component	glutamatergic synapse
A	0106300	biological_process	protein-DNA covalent cross-linking repair
A	0120186	biological_process	negative regulation of protein localization to chromatin
A	0140036	molecular_function	ubiquitin-modified protein reader activity
A	0140455	biological_process	cytoplasm protein quality control
A	1901224	biological_process	positive regulation of non-canonical NF-kappaB signal transduction
A	1903006	biological_process	positive regulation of protein K63-linked deubiquitination
A	1903715	biological_process	regulation of aerobic respiration
A	1903843	biological_process	cellular response to arsenite ion
A	1903862	biological_process	positive regulation of oxidative phosphorylation
A	1904288	molecular_function	BAT3 complex binding
A	1904949	cellular_component	ATPase complex
A	1905634	biological_process	regulation of protein localization to chromatin
A	1990381	molecular_function	ubiquitin-specific protease binding
A	1990730	cellular_component	VCP-NSFL1C complex
A	2000060	biological_process	positive regulation of ubiquitin-dependent protein catabolic process
A	2001171	biological_process	positive regulation of ATP biosynthetic process
B	0000153	cellular_component	cytoplasmic ubiquitin ligase complex
B	0000166	molecular_function	nucleotide binding
B	0000502	cellular_component	proteasome complex
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0005783	cellular_component	endoplasmic reticulum
B	0005789	cellular_component	endoplasmic reticulum membrane
B	0005811	cellular_component	lipid droplet
B	0005829	cellular_component	cytosol
B	0006281	biological_process	DNA repair
B	0006302	biological_process	double-strand break repair
B	0006511	biological_process	ubiquitin-dependent protein catabolic process
B	0006888	biological_process	endoplasmic reticulum to Golgi vesicle-mediated transport
B	0006914	biological_process	autophagy
B	0006974	biological_process	DNA damage response
B	0007249	biological_process	canonical NF-kappaB signal transduction
B	0008289	molecular_function	lipid binding
B	0010494	cellular_component	cytoplasmic stress granule
B	0010498	biological_process	proteasomal protein catabolic process
B	0010918	biological_process	positive regulation of mitochondrial membrane potential
B	0016236	biological_process	macroautophagy
B	0016567	biological_process	protein ubiquitination
B	0016787	molecular_function	hydrolase activity
B	0016887	molecular_function	ATP hydrolysis activity
B	0019079	biological_process	viral genome replication
B	0019674	biological_process	NAD+ metabolic process
B	0019903	molecular_function	protein phosphatase binding
B	0019904	molecular_function	protein domain specific binding
B	0019985	biological_process	translesion synthesis
B	0030970	biological_process	retrograde protein transport, ER to cytosol
B	0031334	biological_process	positive regulation of protein-containing complex assembly
B	0031593	molecular_function	polyubiquitin modification-dependent protein binding
B	0031625	molecular_function	ubiquitin protein ligase binding
B	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
B	0032510	biological_process	endosome to lysosome transport via multivesicular body sorting pathway
B	0032991	cellular_component	protein-containing complex
B	0034098	cellular_component	VCP-NPL4-UFD1 AAA ATPase complex
B	0034605	biological_process	cellular response to heat
B	0035331	biological_process	negative regulation of hippo signaling
B	0035617	biological_process	stress granule disassembly
B	0035800	molecular_function	deubiquitinase activator activity
B	0035861	cellular_component	site of double-strand break
B	0036064	cellular_component	ciliary basal body
B	0036297	biological_process	interstrand cross-link repair
B	0036435	molecular_function	K48-linked polyubiquitin modification-dependent protein binding
B	0036503	biological_process	ERAD pathway
B	0036513	cellular_component	Derlin-1 retrotranslocation complex
B	0042288	molecular_function	MHC class I protein binding
B	0042802	molecular_function	identical protein binding
B	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
B	0043209	cellular_component	myelin sheath
B	0043531	molecular_function	ADP binding
B	0044389	molecular_function	ubiquitin-like protein ligase binding
B	0044877	molecular_function	protein-containing complex binding
B	0045202	cellular_component	synapse
B	0045732	biological_process	positive regulation of protein catabolic process
B	0045879	biological_process	negative regulation of smoothened signaling pathway
B	0046034	biological_process	ATP metabolic process
B	0048471	cellular_component	perinuclear region of cytoplasm
B	0050807	biological_process	regulation of synapse organization
B	0051228	biological_process	mitotic spindle disassembly
B	0061857	biological_process	endoplasmic reticulum stress-induced pre-emptive quality control
B	0070842	biological_process	aggresome assembly
B	0071218	biological_process	cellular response to misfolded protein
B	0072389	biological_process	flavin adenine dinucleotide catabolic process
B	0090263	biological_process	positive regulation of canonical Wnt signaling pathway
B	0097352	biological_process	autophagosome maturation
B	0098978	cellular_component	glutamatergic synapse
B	0106300	biological_process	protein-DNA covalent cross-linking repair
B	0120186	biological_process	negative regulation of protein localization to chromatin
B	0140036	molecular_function	ubiquitin-modified protein reader activity
B	0140455	biological_process	cytoplasm protein quality control
B	1901224	biological_process	positive regulation of non-canonical NF-kappaB signal transduction
B	1903006	biological_process	positive regulation of protein K63-linked deubiquitination
B	1903715	biological_process	regulation of aerobic respiration
B	1903843	biological_process	cellular response to arsenite ion
B	1903862	biological_process	positive regulation of oxidative phosphorylation
B	1904288	molecular_function	BAT3 complex binding
B	1904949	cellular_component	ATPase complex
B	1905634	biological_process	regulation of protein localization to chromatin
B	1990381	molecular_function	ubiquitin-specific protease binding
B	1990730	cellular_component	VCP-NSFL1C complex
B	2000060	biological_process	positive regulation of ubiquitin-dependent protein catabolic process
B	2001171	biological_process	positive regulation of ATP biosynthetic process
C	0000153	cellular_component	cytoplasmic ubiquitin ligase complex
C	0000166	molecular_function	nucleotide binding
C	0000502	cellular_component	proteasome complex
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005783	cellular_component	endoplasmic reticulum
C	0005789	cellular_component	endoplasmic reticulum membrane
C	0005811	cellular_component	lipid droplet
C	0005829	cellular_component	cytosol
C	0006281	biological_process	DNA repair
C	0006302	biological_process	double-strand break repair
C	0006511	biological_process	ubiquitin-dependent protein catabolic process
C	0006888	biological_process	endoplasmic reticulum to Golgi vesicle-mediated transport
C	0006914	biological_process	autophagy
C	0006974	biological_process	DNA damage response
C	0007249	biological_process	canonical NF-kappaB signal transduction
C	0008289	molecular_function	lipid binding
C	0010494	cellular_component	cytoplasmic stress granule
C	0010498	biological_process	proteasomal protein catabolic process
C	0010918	biological_process	positive regulation of mitochondrial membrane potential
C	0016236	biological_process	macroautophagy
C	0016567	biological_process	protein ubiquitination
C	0016787	molecular_function	hydrolase activity
C	0016887	molecular_function	ATP hydrolysis activity
C	0019079	biological_process	viral genome replication
C	0019674	biological_process	NAD+ metabolic process
C	0019903	molecular_function	protein phosphatase binding
C	0019904	molecular_function	protein domain specific binding
C	0019985	biological_process	translesion synthesis
C	0030970	biological_process	retrograde protein transport, ER to cytosol
C	0031334	biological_process	positive regulation of protein-containing complex assembly
C	0031593	molecular_function	polyubiquitin modification-dependent protein binding
C	0031625	molecular_function	ubiquitin protein ligase binding
C	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
C	0032510	biological_process	endosome to lysosome transport via multivesicular body sorting pathway
C	0032991	cellular_component	protein-containing complex
C	0034098	cellular_component	VCP-NPL4-UFD1 AAA ATPase complex
C	0034605	biological_process	cellular response to heat
C	0035331	biological_process	negative regulation of hippo signaling
C	0035617	biological_process	stress granule disassembly
C	0035800	molecular_function	deubiquitinase activator activity
C	0035861	cellular_component	site of double-strand break
C	0036064	cellular_component	ciliary basal body
C	0036297	biological_process	interstrand cross-link repair
C	0036435	molecular_function	K48-linked polyubiquitin modification-dependent protein binding
C	0036503	biological_process	ERAD pathway
C	0036513	cellular_component	Derlin-1 retrotranslocation complex
C	0042288	molecular_function	MHC class I protein binding
C	0042802	molecular_function	identical protein binding
C	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
C	0043209	cellular_component	myelin sheath
C	0043531	molecular_function	ADP binding
C	0044389	molecular_function	ubiquitin-like protein ligase binding
C	0044877	molecular_function	protein-containing complex binding
C	0045202	cellular_component	synapse
C	0045732	biological_process	positive regulation of protein catabolic process
C	0045879	biological_process	negative regulation of smoothened signaling pathway
C	0046034	biological_process	ATP metabolic process
C	0048471	cellular_component	perinuclear region of cytoplasm
C	0050807	biological_process	regulation of synapse organization
C	0051228	biological_process	mitotic spindle disassembly
C	0061857	biological_process	endoplasmic reticulum stress-induced pre-emptive quality control
C	0070842	biological_process	aggresome assembly
C	0071218	biological_process	cellular response to misfolded protein
C	0072389	biological_process	flavin adenine dinucleotide catabolic process
C	0090263	biological_process	positive regulation of canonical Wnt signaling pathway
C	0097352	biological_process	autophagosome maturation
C	0098978	cellular_component	glutamatergic synapse
C	0106300	biological_process	protein-DNA covalent cross-linking repair
C	0120186	biological_process	negative regulation of protein localization to chromatin
C	0140036	molecular_function	ubiquitin-modified protein reader activity
C	0140455	biological_process	cytoplasm protein quality control
C	1901224	biological_process	positive regulation of non-canonical NF-kappaB signal transduction
C	1903006	biological_process	positive regulation of protein K63-linked deubiquitination
C	1903715	biological_process	regulation of aerobic respiration
C	1903843	biological_process	cellular response to arsenite ion
C	1903862	biological_process	positive regulation of oxidative phosphorylation
C	1904288	molecular_function	BAT3 complex binding
C	1904949	cellular_component	ATPase complex
C	1905634	biological_process	regulation of protein localization to chromatin
C	1990381	molecular_function	ubiquitin-specific protease binding
C	1990730	cellular_component	VCP-NSFL1C complex
C	2000060	biological_process	positive regulation of ubiquitin-dependent protein catabolic process
C	2001171	biological_process	positive regulation of ATP biosynthetic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	13
Details	BINDING SITE FOR RESIDUE ADP A 807

Chain	Residue
A	ASP205
A	HIS384
A	GLY408
A	ALA409
C	ARG359
A	ILE206
A	GLY207
A	GLY248
A	THR249
A	GLY250
A	LYS251
A	THR252
A	LEU253

---

site_id	AC2
Number of Residues	11
Details	BINDING SITE FOR RESIDUE ADP A 900

Chain	Residue
A	ASP478
A	ILE479
A	CYS522
A	GLY523
A	LYS524
A	THR525
A	LEU526
A	ILE656
A	GLY684
A	ALA685
A	THR688

---

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE AF3 A 915

Chain	Residue
A	PRO519
A	PRO520
A	GLY521
A	CYS522
A	LYS524
A	THR525

---

site_id	AC4
Number of Residues	12
Details	BINDING SITE FOR RESIDUE ADP B 807

Chain	Residue
A	ARG359
B	ASP205
B	GLY207
B	GLY248
B	THR249
B	GLY250
B	LYS251
B	THR252
B	LEU253
B	ASP304
B	HIS384
B	GLY408

---

site_id	AC5
Number of Residues	13
Details	BINDING SITE FOR RESIDUE ADP B 900

Chain	Residue
B	ASP478
B	ILE479
B	GLY521
B	CYS522
B	GLY523
B	LYS524
B	THR525
B	LEU526
B	ILE656
B	ASN660
B	GLY684
B	ALA685
B	THR688

---

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE AF3 B 915

Chain	Residue
B	PRO519
B	PRO520
B	GLY521
B	CYS522
B	GLY523
B	LYS524

---

site_id	AC7
Number of Residues	14
Details	BINDING SITE FOR RESIDUE ADP C 807

Chain	Residue
B	ARG359
C	ASP205
C	ILE206
C	GLY207
C	PRO247
C	GLY248
C	THR249
C	GLY250
C	LYS251
C	THR252
C	LEU253
C	HIS384
C	GLY408
C	ALA409

---

site_id	AC8
Number of Residues	13
Details	BINDING SITE FOR RESIDUE ADP C 900

Chain	Residue
C	ASP478
C	ILE479
C	GLY521
C	CYS522
C	GLY523
C	LYS524
C	THR525
C	LEU526
C	ILE656
C	ASN660
C	GLY684
C	ALA685
C	THR688

---

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE AF3 C 915

Chain	Residue
C	PRO519
C	PRO520
C	GLY521
C	CYS522
C	GLY523
C	LYS524

---

Functional Information from PROSITE/UniProt

site_id	PS00674
Number of Residues	19
Details	AAA AAA-protein family signature. ViVMaATNrpnsIDpALr.R

Chain	Residue	Details
A	VAL341-ARG359
A	VAL617-ARG635

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	36
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11163219","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"14988733","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P55072","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	9
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P55072","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	3
Details	Modified residue: {"description":"N6,N6,N6-trimethyllysine; by VCPKMT","evidences":[{"source":"PubMed","id":"22948820","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	3
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P55072","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	9
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"23806337","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	3
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"23806337","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---