Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

6OAB

Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 2

Functional Information from GO Data
ChainGOidnamespacecontents
A0000837cellular_componentDoa10p ubiquitin ligase complex
A0000839cellular_componentHrd1p ubiquitin ligase ERAD-L complex
A0003689molecular_functionDNA clamp loader activity
A0005515molecular_functionprotein binding
A0005524molecular_functionATP binding
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0005783cellular_componentendoplasmic reticulum
A0005789cellular_componentendoplasmic reticulum membrane
A0005829cellular_componentcytosol
A0006274biological_processDNA replication termination
A0006338biological_processchromatin remodeling
A0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
A0010636biological_processpositive regulation of mitochondrial fusion
A0015031biological_processprotein transport
A0016236biological_processmacroautophagy
A0016320biological_processendoplasmic reticulum membrane fusion
A0016787molecular_functionhydrolase activity
A0016887molecular_functionATP hydrolysis activity
A0019888molecular_functionprotein phosphatase regulator activity
A0030894cellular_componentreplisome
A0030970biological_processretrograde protein transport, ER to cytosol
A0031134biological_processsister chromatid biorientation
A0031593molecular_functionpolyubiquitin modification-dependent protein binding
A0032984biological_processprotein-containing complex disassembly
A0034098cellular_componentVCP-NPL4-UFD1 AAA ATPase complex
A0034517biological_processribophagy
A0034727biological_processpiecemeal microautophagy of the nucleus
A0036266cellular_componentCdc48p-Npl4p-Vms1p AAA ATPase complex
A0036503biological_processERAD pathway
A0042802molecular_functionidentical protein binding
A0043130molecular_functionubiquitin binding
A0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
A0043231cellular_componentintracellular membrane-bounded organelle
A0043328biological_processprotein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
A0043332cellular_componentmating projection tip
A0046034biological_processATP metabolic process
A0051228biological_processmitotic spindle disassembly
A0061775molecular_functioncohesin loader activity
A0070651biological_processnonfunctional rRNA decay
A0071629biological_processcytoplasm protein quality control by the ubiquitin-proteasome system
A0071630biological_processnuclear protein quality control by the ubiquitin-proteasome system
A0072344biological_processrescue of stalled ribosome
A0072671biological_processmitochondria-associated ubiquitin-dependent protein catabolic process
A0097352biological_processautophagosome maturation
A0099638biological_processendosome to plasma membrane protein transport
A0120174biological_processstress-induced homeostatically regulated protein degradation pathway
A0140584molecular_functionchromatin extrusion motor activity
A0140588biological_processchromatin looping
A0140665molecular_functionATP-dependent H3-H4 histone complex chaperone activity
A0140849molecular_functionATP-dependent H2AZ histone chaperone activity
A1900182biological_processpositive regulation of protein localization to nucleus
A1902979biological_processmitotic DNA replication termination
A1990112cellular_componentRQC complex
A1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
A1990171biological_processSCF complex disassembly in response to cadmium stress
B0000837cellular_componentDoa10p ubiquitin ligase complex
B0000839cellular_componentHrd1p ubiquitin ligase ERAD-L complex
B0003689molecular_functionDNA clamp loader activity
B0005515molecular_functionprotein binding
B0005524molecular_functionATP binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005739cellular_componentmitochondrion
B0005783cellular_componentendoplasmic reticulum
B0005789cellular_componentendoplasmic reticulum membrane
B0005829cellular_componentcytosol
B0006274biological_processDNA replication termination
B0006338biological_processchromatin remodeling
B0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
B0010636biological_processpositive regulation of mitochondrial fusion
B0015031biological_processprotein transport
B0016236biological_processmacroautophagy
B0016320biological_processendoplasmic reticulum membrane fusion
B0016787molecular_functionhydrolase activity
B0016887molecular_functionATP hydrolysis activity
B0019888molecular_functionprotein phosphatase regulator activity
B0030894cellular_componentreplisome
B0030970biological_processretrograde protein transport, ER to cytosol
B0031134biological_processsister chromatid biorientation
B0031593molecular_functionpolyubiquitin modification-dependent protein binding
B0032984biological_processprotein-containing complex disassembly
B0034098cellular_componentVCP-NPL4-UFD1 AAA ATPase complex
B0034517biological_processribophagy
B0034727biological_processpiecemeal microautophagy of the nucleus
B0036266cellular_componentCdc48p-Npl4p-Vms1p AAA ATPase complex
B0036503biological_processERAD pathway
B0042802molecular_functionidentical protein binding
B0043130molecular_functionubiquitin binding
B0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
B0043231cellular_componentintracellular membrane-bounded organelle
B0043328biological_processprotein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
B0043332cellular_componentmating projection tip
B0046034biological_processATP metabolic process
B0051228biological_processmitotic spindle disassembly
B0061775molecular_functioncohesin loader activity
B0070651biological_processnonfunctional rRNA decay
B0071629biological_processcytoplasm protein quality control by the ubiquitin-proteasome system
B0071630biological_processnuclear protein quality control by the ubiquitin-proteasome system
B0072344biological_processrescue of stalled ribosome
B0072671biological_processmitochondria-associated ubiquitin-dependent protein catabolic process
B0097352biological_processautophagosome maturation
B0099638biological_processendosome to plasma membrane protein transport
B0120174biological_processstress-induced homeostatically regulated protein degradation pathway
B0140584molecular_functionchromatin extrusion motor activity
B0140588biological_processchromatin looping
B0140665molecular_functionATP-dependent H3-H4 histone complex chaperone activity
B0140849molecular_functionATP-dependent H2AZ histone chaperone activity
B1900182biological_processpositive regulation of protein localization to nucleus
B1902979biological_processmitotic DNA replication termination
B1990112cellular_componentRQC complex
B1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
B1990171biological_processSCF complex disassembly in response to cadmium stress
C0000837cellular_componentDoa10p ubiquitin ligase complex
C0000839cellular_componentHrd1p ubiquitin ligase ERAD-L complex
C0003689molecular_functionDNA clamp loader activity
C0005515molecular_functionprotein binding
C0005524molecular_functionATP binding
C0005634cellular_componentnucleus
C0005737cellular_componentcytoplasm
C0005739cellular_componentmitochondrion
C0005783cellular_componentendoplasmic reticulum
C0005789cellular_componentendoplasmic reticulum membrane
C0005829cellular_componentcytosol
C0006274biological_processDNA replication termination
C0006338biological_processchromatin remodeling
C0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
C0010636biological_processpositive regulation of mitochondrial fusion
C0015031biological_processprotein transport
C0016236biological_processmacroautophagy
C0016320biological_processendoplasmic reticulum membrane fusion
C0016787molecular_functionhydrolase activity
C0016887molecular_functionATP hydrolysis activity
C0019888molecular_functionprotein phosphatase regulator activity
C0030894cellular_componentreplisome
C0030970biological_processretrograde protein transport, ER to cytosol
C0031134biological_processsister chromatid biorientation
C0031593molecular_functionpolyubiquitin modification-dependent protein binding
C0032984biological_processprotein-containing complex disassembly
C0034098cellular_componentVCP-NPL4-UFD1 AAA ATPase complex
C0034517biological_processribophagy
C0034727biological_processpiecemeal microautophagy of the nucleus
C0036266cellular_componentCdc48p-Npl4p-Vms1p AAA ATPase complex
C0036503biological_processERAD pathway
C0042802molecular_functionidentical protein binding
C0043130molecular_functionubiquitin binding
C0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
C0043231cellular_componentintracellular membrane-bounded organelle
C0043328biological_processprotein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
C0043332cellular_componentmating projection tip
C0046034biological_processATP metabolic process
C0051228biological_processmitotic spindle disassembly
C0061775molecular_functioncohesin loader activity
C0070651biological_processnonfunctional rRNA decay
C0071629biological_processcytoplasm protein quality control by the ubiquitin-proteasome system
C0071630biological_processnuclear protein quality control by the ubiquitin-proteasome system
C0072344biological_processrescue of stalled ribosome
C0072671biological_processmitochondria-associated ubiquitin-dependent protein catabolic process
C0097352biological_processautophagosome maturation
C0099638biological_processendosome to plasma membrane protein transport
C0120174biological_processstress-induced homeostatically regulated protein degradation pathway
C0140584molecular_functionchromatin extrusion motor activity
C0140588biological_processchromatin looping
C0140665molecular_functionATP-dependent H3-H4 histone complex chaperone activity
C0140849molecular_functionATP-dependent H2AZ histone chaperone activity
C1900182biological_processpositive regulation of protein localization to nucleus
C1902979biological_processmitotic DNA replication termination
C1990112cellular_componentRQC complex
C1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
C1990171biological_processSCF complex disassembly in response to cadmium stress
D0000837cellular_componentDoa10p ubiquitin ligase complex
D0000839cellular_componentHrd1p ubiquitin ligase ERAD-L complex
D0003689molecular_functionDNA clamp loader activity
D0005515molecular_functionprotein binding
D0005524molecular_functionATP binding
D0005634cellular_componentnucleus
D0005737cellular_componentcytoplasm
D0005739cellular_componentmitochondrion
D0005783cellular_componentendoplasmic reticulum
D0005789cellular_componentendoplasmic reticulum membrane
D0005829cellular_componentcytosol
D0006274biological_processDNA replication termination
D0006338biological_processchromatin remodeling
D0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
D0010636biological_processpositive regulation of mitochondrial fusion
D0015031biological_processprotein transport
D0016236biological_processmacroautophagy
D0016320biological_processendoplasmic reticulum membrane fusion
D0016787molecular_functionhydrolase activity
D0016887molecular_functionATP hydrolysis activity
D0019888molecular_functionprotein phosphatase regulator activity
D0030894cellular_componentreplisome
D0030970biological_processretrograde protein transport, ER to cytosol
D0031134biological_processsister chromatid biorientation
D0031593molecular_functionpolyubiquitin modification-dependent protein binding
D0032984biological_processprotein-containing complex disassembly
D0034098cellular_componentVCP-NPL4-UFD1 AAA ATPase complex
D0034517biological_processribophagy
D0034727biological_processpiecemeal microautophagy of the nucleus
D0036266cellular_componentCdc48p-Npl4p-Vms1p AAA ATPase complex
D0036503biological_processERAD pathway
D0042802molecular_functionidentical protein binding
D0043130molecular_functionubiquitin binding
D0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
D0043231cellular_componentintracellular membrane-bounded organelle
D0043328biological_processprotein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
D0043332cellular_componentmating projection tip
D0046034biological_processATP metabolic process
D0051228biological_processmitotic spindle disassembly
D0061775molecular_functioncohesin loader activity
D0070651biological_processnonfunctional rRNA decay
D0071629biological_processcytoplasm protein quality control by the ubiquitin-proteasome system
D0071630biological_processnuclear protein quality control by the ubiquitin-proteasome system
D0072344biological_processrescue of stalled ribosome
D0072671biological_processmitochondria-associated ubiquitin-dependent protein catabolic process
D0097352biological_processautophagosome maturation
D0099638biological_processendosome to plasma membrane protein transport
D0120174biological_processstress-induced homeostatically regulated protein degradation pathway
D0140584molecular_functionchromatin extrusion motor activity
D0140588biological_processchromatin looping
D0140665molecular_functionATP-dependent H3-H4 histone complex chaperone activity
D0140849molecular_functionATP-dependent H2AZ histone chaperone activity
D1900182biological_processpositive regulation of protein localization to nucleus
D1902979biological_processmitotic DNA replication termination
D1990112cellular_componentRQC complex
D1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
D1990171biological_processSCF complex disassembly in response to cadmium stress
E0000837cellular_componentDoa10p ubiquitin ligase complex
E0000839cellular_componentHrd1p ubiquitin ligase ERAD-L complex
E0003689molecular_functionDNA clamp loader activity
E0005515molecular_functionprotein binding
E0005524molecular_functionATP binding
E0005634cellular_componentnucleus
E0005737cellular_componentcytoplasm
E0005739cellular_componentmitochondrion
E0005783cellular_componentendoplasmic reticulum
E0005789cellular_componentendoplasmic reticulum membrane
E0005829cellular_componentcytosol
E0006274biological_processDNA replication termination
E0006338biological_processchromatin remodeling
E0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
E0010636biological_processpositive regulation of mitochondrial fusion
E0015031biological_processprotein transport
E0016236biological_processmacroautophagy
E0016320biological_processendoplasmic reticulum membrane fusion
E0016787molecular_functionhydrolase activity
E0016887molecular_functionATP hydrolysis activity
E0019888molecular_functionprotein phosphatase regulator activity
E0030894cellular_componentreplisome
E0030970biological_processretrograde protein transport, ER to cytosol
E0031134biological_processsister chromatid biorientation
E0031593molecular_functionpolyubiquitin modification-dependent protein binding
E0032984biological_processprotein-containing complex disassembly
E0034098cellular_componentVCP-NPL4-UFD1 AAA ATPase complex
E0034517biological_processribophagy
E0034727biological_processpiecemeal microautophagy of the nucleus
E0036266cellular_componentCdc48p-Npl4p-Vms1p AAA ATPase complex
E0036503biological_processERAD pathway
E0042802molecular_functionidentical protein binding
E0043130molecular_functionubiquitin binding
E0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
E0043231cellular_componentintracellular membrane-bounded organelle
E0043328biological_processprotein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
E0043332cellular_componentmating projection tip
E0046034biological_processATP metabolic process
E0051228biological_processmitotic spindle disassembly
E0061775molecular_functioncohesin loader activity
E0070651biological_processnonfunctional rRNA decay
E0071629biological_processcytoplasm protein quality control by the ubiquitin-proteasome system
E0071630biological_processnuclear protein quality control by the ubiquitin-proteasome system
E0072344biological_processrescue of stalled ribosome
E0072671biological_processmitochondria-associated ubiquitin-dependent protein catabolic process
E0097352biological_processautophagosome maturation
E0099638biological_processendosome to plasma membrane protein transport
E0120174biological_processstress-induced homeostatically regulated protein degradation pathway
E0140584molecular_functionchromatin extrusion motor activity
E0140588biological_processchromatin looping
E0140665molecular_functionATP-dependent H3-H4 histone complex chaperone activity
E0140849molecular_functionATP-dependent H2AZ histone chaperone activity
E1900182biological_processpositive regulation of protein localization to nucleus
E1902979biological_processmitotic DNA replication termination
E1990112cellular_componentRQC complex
E1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
E1990171biological_processSCF complex disassembly in response to cadmium stress
Functional Information from PDB Data
site_idAC1
Number of Residues12
Detailsbinding site for residue ADP D 901
ChainResidue
DGLY217
DGLY418
DBEF902
EARG369
DGLY258
DTHR259
DGLY260
DLYS261
DTHR262
DLEU263
DVAL390
DHIS394

site_idAC2
Number of Residues6
Detailsbinding site for residue BEF D 902
ChainResidue
DTHR262
DASP314
DGLU315
DADP901
EASP343
EARG372

site_idAC3
Number of Residues6
Detailsbinding site for residue BEF D 903
ChainResidue
DLYS534
DTHR535
DASP587
DGLU588
DALA632
DADP904

site_idAC4
Number of Residues10
Detailsbinding site for residue ADP D 904
ChainResidue
DASP488
DVAL489
DGLY533
DLYS534
DTHR535
DLEU536
DGLN670
DBEF903
EARG645
EARG648

site_idAC5
Number of Residues7
Detailsbinding site for residue ADP E 901
ChainResidue
EPRO530
EGLY531
ETHR532
EGLY533
ELYS534
ETHR535
ELEU536

site_idAC6
Number of Residues8
Detailsbinding site for residue ADP E 902
ChainResidue
EILE216
ETHR259
EGLY260
ELYS261
ETHR262
ELEU263
EMET264
EVAL390

site_idAC7
Number of Residues14
Detailsbinding site for residue ADP B 901
ChainResidue
BASP488
BVAL489
BPRO530
BGLY531
BTHR532
BGLY533
BLYS534
BTHR535
BLEU536
BILE666
BGLN670
BBEF904
CARG645
CARG648

site_idAC8
Number of Residues5
Detailsbinding site for residue BEF B 902
ChainResidue
AASP314
AADP902
BASP343
BARG369
BARG372

site_idAC9
Number of Residues5
Detailsbinding site for residue BEF B 903
ChainResidue
BTHR262
BASP314
BGLU315
BALA356
BADP905

site_idAD1
Number of Residues6
Detailsbinding site for residue BEF B 904
ChainResidue
BLYS534
BTHR535
BASP587
BGLU588
BADP901
CARG648

site_idAD2
Number of Residues12
Detailsbinding site for residue ADP B 905
ChainResidue
BILE216
BGLY217
BPRO257
BGLY260
BLYS261
BTHR262
BLEU263
BGLY418
BBEF903
CARG369
CPHE370
CARG372

site_idAD3
Number of Residues7
Detailsbinding site for residue BEF C 903
ChainResidue
CLYS261
CTHR262
CASP314
CGLU315
CALA356
CADP901
DARG372

site_idAD4
Number of Residues7
Detailsbinding site for residue BEF A 903
ChainResidue
AASP587
AGLU588
AALA632
AASN634
AADP901
BARG648
ATHR535

site_idAD5
Number of Residues16
Detailsbinding site for residue ADP A 901
ChainResidue
AGLY490
AGLY531
ATHR532
AGLY533
ALYS534
ATHR535
ALEU537
AALA538
ALYS539
AALA540
AILE666
AGLY694
ABEF903
BASP619
BARG645
BARG648

site_idAD6
Number of Residues16
Detailsbinding site for residue ADP A 901
ChainResidue
AGLY490
AGLY531
ATHR532
AGLY533
ALYS534
ATHR535
ALEU537
AALA538
ALYS539
AALA540
AILE666
AGLY694
ABEF903
BASP619
BARG645
BARG648

site_idAD7
Number of Residues10
Detailsbinding site for residue ADP A 902
ChainResidue
APRO256
AGLY258
AGLY260
ALYS261
ATHR262
ALEU263
AASP314
AVAL390
BARG369
BBEF902

site_idAD8
Number of Residues21
Detailsbinding site for residue ADP C 901
ChainResidue
CILE216
CGLY217
CGLY258
CTHR259
CGLY260
CLYS261
CTHR262
CLEU263
CVAL390
CLEU391
CARG392
CILE393
CTHR395
CMET398
CGLY418
CALA422
CCYS425
CBEF903
DASP343
DARG369
DARG372

site_idAD9
Number of Residues14
Detailsbinding site for residue ADP C 902
ChainResidue
CVAL489
CGLY490
CPRO530
CGLY531
CTHR532
CGLY533
CTHR535
CLEU536
CTHR633
CILE666
CGLN670
CGLY694
CBEF904
DARG645

site_idAE1
Number of Residues16
Detailsbinding site for residue ADP C 902
ChainResidue
CVAL489
CGLY490
CPRO530
CGLY531
CTHR532
CGLY533
CLYS534
CLEU536
CLEU537
CALA538
CASP587
CILE666
CGLN670
CGLY694
CBEF904
DARG645

site_idAE2
Number of Residues8
Detailsbinding site for residue BEF C 904
ChainResidue
CLYS534
CLEU536
CLEU537
CALA538
CASP587
CGLU588
CADP902
DARG648

Functional Information from PROSITE/UniProt
site_idPS00430
Number of Residues72
DetailsTONB_DEPENDENT_REC_1 TonB-dependent receptor (TBDR) proteins signature 1. mgeehkplldasgvdpreedktatailrrkkkdnmllvddainddnsviainsntmdklelfrg...................................................DTVLVKGK
ChainResidueDetails
DMET1-LYS72

site_idPS00674
Number of Residues19
DetailsAAA AAA-protein family signature. VvVIaATNrpnsIDpALr.R
ChainResidueDetails
DVAL351-ARG369
DVAL627-ARG645

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues15
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:P55072
ChainResidueDetails
DPRO257
CPRO257
CASN358
CHIS394
APRO257
AASN358
AHIS394
DASN358
DHIS394
EPRO257
EASN358
EHIS394
BPRO257
BASN358
BHIS394

site_idSWS_FT_FI2
Number of Residues5
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:Q01853
ChainResidueDetails
DGLY531
EGLY531
BGLY531
CGLY531
AGLY531

site_idSWS_FT_FI3
Number of Residues5
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:18407956
ChainResidueDetails
DSER472
ESER472
BSER472
CSER472
ASER472

site_idSWS_FT_FI4
Number of Residues5
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:17330950, ECO:0007744|PubMed:19779198
ChainResidueDetails
DSER519
ESER519
BSER519
CSER519
ASER519

site_idSWS_FT_FI5
Number of Residues5
DetailsMOD_RES: Phosphothreonine => ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198
ChainResidueDetails
DTHR735
ETHR735
BTHR735
CTHR735
ATHR735

site_idSWS_FT_FI6
Number of Residues5
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:17287358, ECO:0007744|PubMed:17330950
ChainResidueDetails
DSER770
ESER770
BSER770
CSER770
ASER770

site_idSWS_FT_FI7
Number of Residues25
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0007744|PubMed:22106047
ChainResidueDetails
DLYS305
ELYS539
BLYS305
BLYS322
BLYS346
BLYS522
BLYS539
CLYS305
CLYS322
CLYS346
CLYS522
DLYS322
CLYS539
ALYS305
ALYS322
ALYS346
ALYS522
ALYS539
DLYS346
DLYS522
DLYS539
ELYS305
ELYS322
ELYS346
ELYS522

site_idSWS_FT_FI8
Number of Residues15
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:12872131
ChainResidueDetails
CLYS594
CLYS673
ALYS594
ALYS673
DLYS594
DLYS673
ELYS594
ELYS673
BLYS594
BLYS673

227111

PDB entries from 2024-11-06

PDB statisticsPDBj update infoContact PDBjnumon