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6NB1

Crystal structure of Escherichia coli ClpP protease complexed with small molecule activator, ACP1-06

Functional Information from GO Data
ChainGOidnamespacecontents
A0004176molecular_functionATP-dependent peptidase activity
A0004252molecular_functionserine-type endopeptidase activity
A0005515molecular_functionprotein binding
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0006508biological_processproteolysis
A0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
A0008236molecular_functionserine-type peptidase activity
A0009266biological_processresponse to temperature stimulus
A0009314biological_processresponse to radiation
A0009368cellular_componentendopeptidase Clp complex
A0009376cellular_componentHslUV protease complex
A0009408biological_processresponse to heat
A0010498biological_processproteasomal protein catabolic process
A0016020cellular_componentmembrane
A0042802molecular_functionidentical protein binding
A0043068biological_processpositive regulation of programmed cell death
A0051117molecular_functionATPase binding
B0004176molecular_functionATP-dependent peptidase activity
B0004252molecular_functionserine-type endopeptidase activity
B0005515molecular_functionprotein binding
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0006508biological_processproteolysis
B0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
B0008236molecular_functionserine-type peptidase activity
B0009266biological_processresponse to temperature stimulus
B0009314biological_processresponse to radiation
B0009368cellular_componentendopeptidase Clp complex
B0009376cellular_componentHslUV protease complex
B0009408biological_processresponse to heat
B0010498biological_processproteasomal protein catabolic process
B0016020cellular_componentmembrane
B0042802molecular_functionidentical protein binding
B0043068biological_processpositive regulation of programmed cell death
B0051117molecular_functionATPase binding
C0004176molecular_functionATP-dependent peptidase activity
C0004252molecular_functionserine-type endopeptidase activity
C0005515molecular_functionprotein binding
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0006508biological_processproteolysis
C0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
C0008236molecular_functionserine-type peptidase activity
C0009266biological_processresponse to temperature stimulus
C0009314biological_processresponse to radiation
C0009368cellular_componentendopeptidase Clp complex
C0009376cellular_componentHslUV protease complex
C0009408biological_processresponse to heat
C0010498biological_processproteasomal protein catabolic process
C0016020cellular_componentmembrane
C0042802molecular_functionidentical protein binding
C0043068biological_processpositive regulation of programmed cell death
C0051117molecular_functionATPase binding
D0004176molecular_functionATP-dependent peptidase activity
D0004252molecular_functionserine-type endopeptidase activity
D0005515molecular_functionprotein binding
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0006508biological_processproteolysis
D0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
D0008236molecular_functionserine-type peptidase activity
D0009266biological_processresponse to temperature stimulus
D0009314biological_processresponse to radiation
D0009368cellular_componentendopeptidase Clp complex
D0009376cellular_componentHslUV protease complex
D0009408biological_processresponse to heat
D0010498biological_processproteasomal protein catabolic process
D0016020cellular_componentmembrane
D0042802molecular_functionidentical protein binding
D0043068biological_processpositive regulation of programmed cell death
D0051117molecular_functionATPase binding
E0004176molecular_functionATP-dependent peptidase activity
E0004252molecular_functionserine-type endopeptidase activity
E0005515molecular_functionprotein binding
E0005737cellular_componentcytoplasm
E0005829cellular_componentcytosol
E0006508biological_processproteolysis
E0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
E0008236molecular_functionserine-type peptidase activity
E0009266biological_processresponse to temperature stimulus
E0009314biological_processresponse to radiation
E0009368cellular_componentendopeptidase Clp complex
E0009376cellular_componentHslUV protease complex
E0009408biological_processresponse to heat
E0010498biological_processproteasomal protein catabolic process
E0016020cellular_componentmembrane
E0042802molecular_functionidentical protein binding
E0043068biological_processpositive regulation of programmed cell death
E0051117molecular_functionATPase binding
F0004176molecular_functionATP-dependent peptidase activity
F0004252molecular_functionserine-type endopeptidase activity
F0005515molecular_functionprotein binding
F0005737cellular_componentcytoplasm
F0005829cellular_componentcytosol
F0006508biological_processproteolysis
F0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
F0008236molecular_functionserine-type peptidase activity
F0009266biological_processresponse to temperature stimulus
F0009314biological_processresponse to radiation
F0009368cellular_componentendopeptidase Clp complex
F0009376cellular_componentHslUV protease complex
F0009408biological_processresponse to heat
F0010498biological_processproteasomal protein catabolic process
F0016020cellular_componentmembrane
F0042802molecular_functionidentical protein binding
F0043068biological_processpositive regulation of programmed cell death
F0051117molecular_functionATPase binding
G0004176molecular_functionATP-dependent peptidase activity
G0004252molecular_functionserine-type endopeptidase activity
G0005515molecular_functionprotein binding
G0005737cellular_componentcytoplasm
G0005829cellular_componentcytosol
G0006508biological_processproteolysis
G0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
G0008236molecular_functionserine-type peptidase activity
G0009266biological_processresponse to temperature stimulus
G0009314biological_processresponse to radiation
G0009368cellular_componentendopeptidase Clp complex
G0009376cellular_componentHslUV protease complex
G0009408biological_processresponse to heat
G0010498biological_processproteasomal protein catabolic process
G0016020cellular_componentmembrane
G0042802molecular_functionidentical protein binding
G0043068biological_processpositive regulation of programmed cell death
G0051117molecular_functionATPase binding
H0004176molecular_functionATP-dependent peptidase activity
H0004252molecular_functionserine-type endopeptidase activity
H0005515molecular_functionprotein binding
H0005737cellular_componentcytoplasm
H0005829cellular_componentcytosol
H0006508biological_processproteolysis
H0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
H0008236molecular_functionserine-type peptidase activity
H0009266biological_processresponse to temperature stimulus
H0009314biological_processresponse to radiation
H0009368cellular_componentendopeptidase Clp complex
H0009376cellular_componentHslUV protease complex
H0009408biological_processresponse to heat
H0010498biological_processproteasomal protein catabolic process
H0016020cellular_componentmembrane
H0042802molecular_functionidentical protein binding
H0043068biological_processpositive regulation of programmed cell death
H0051117molecular_functionATPase binding
I0004176molecular_functionATP-dependent peptidase activity
I0004252molecular_functionserine-type endopeptidase activity
I0005515molecular_functionprotein binding
I0005737cellular_componentcytoplasm
I0005829cellular_componentcytosol
I0006508biological_processproteolysis
I0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
I0008236molecular_functionserine-type peptidase activity
I0009266biological_processresponse to temperature stimulus
I0009314biological_processresponse to radiation
I0009368cellular_componentendopeptidase Clp complex
I0009376cellular_componentHslUV protease complex
I0009408biological_processresponse to heat
I0010498biological_processproteasomal protein catabolic process
I0016020cellular_componentmembrane
I0042802molecular_functionidentical protein binding
I0043068biological_processpositive regulation of programmed cell death
I0051117molecular_functionATPase binding
J0004176molecular_functionATP-dependent peptidase activity
J0004252molecular_functionserine-type endopeptidase activity
J0005515molecular_functionprotein binding
J0005737cellular_componentcytoplasm
J0005829cellular_componentcytosol
J0006508biological_processproteolysis
J0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
J0008236molecular_functionserine-type peptidase activity
J0009266biological_processresponse to temperature stimulus
J0009314biological_processresponse to radiation
J0009368cellular_componentendopeptidase Clp complex
J0009376cellular_componentHslUV protease complex
J0009408biological_processresponse to heat
J0010498biological_processproteasomal protein catabolic process
J0016020cellular_componentmembrane
J0042802molecular_functionidentical protein binding
J0043068biological_processpositive regulation of programmed cell death
J0051117molecular_functionATPase binding
K0004176molecular_functionATP-dependent peptidase activity
K0004252molecular_functionserine-type endopeptidase activity
K0005515molecular_functionprotein binding
K0005737cellular_componentcytoplasm
K0005829cellular_componentcytosol
K0006508biological_processproteolysis
K0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
K0008236molecular_functionserine-type peptidase activity
K0009266biological_processresponse to temperature stimulus
K0009314biological_processresponse to radiation
K0009368cellular_componentendopeptidase Clp complex
K0009376cellular_componentHslUV protease complex
K0009408biological_processresponse to heat
K0010498biological_processproteasomal protein catabolic process
K0016020cellular_componentmembrane
K0042802molecular_functionidentical protein binding
K0043068biological_processpositive regulation of programmed cell death
K0051117molecular_functionATPase binding
L0004176molecular_functionATP-dependent peptidase activity
L0004252molecular_functionserine-type endopeptidase activity
L0005515molecular_functionprotein binding
L0005737cellular_componentcytoplasm
L0005829cellular_componentcytosol
L0006508biological_processproteolysis
L0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
L0008236molecular_functionserine-type peptidase activity
L0009266biological_processresponse to temperature stimulus
L0009314biological_processresponse to radiation
L0009368cellular_componentendopeptidase Clp complex
L0009376cellular_componentHslUV protease complex
L0009408biological_processresponse to heat
L0010498biological_processproteasomal protein catabolic process
L0016020cellular_componentmembrane
L0042802molecular_functionidentical protein binding
L0043068biological_processpositive regulation of programmed cell death
L0051117molecular_functionATPase binding
M0004176molecular_functionATP-dependent peptidase activity
M0004252molecular_functionserine-type endopeptidase activity
M0005515molecular_functionprotein binding
M0005737cellular_componentcytoplasm
M0005829cellular_componentcytosol
M0006508biological_processproteolysis
M0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
M0008236molecular_functionserine-type peptidase activity
M0009266biological_processresponse to temperature stimulus
M0009314biological_processresponse to radiation
M0009368cellular_componentendopeptidase Clp complex
M0009376cellular_componentHslUV protease complex
M0009408biological_processresponse to heat
M0010498biological_processproteasomal protein catabolic process
M0016020cellular_componentmembrane
M0042802molecular_functionidentical protein binding
M0043068biological_processpositive regulation of programmed cell death
M0051117molecular_functionATPase binding
N0004176molecular_functionATP-dependent peptidase activity
N0004252molecular_functionserine-type endopeptidase activity
N0005515molecular_functionprotein binding
N0005737cellular_componentcytoplasm
N0005829cellular_componentcytosol
N0006508biological_processproteolysis
N0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
N0008236molecular_functionserine-type peptidase activity
N0009266biological_processresponse to temperature stimulus
N0009314biological_processresponse to radiation
N0009368cellular_componentendopeptidase Clp complex
N0009376cellular_componentHslUV protease complex
N0009408biological_processresponse to heat
N0010498biological_processproteasomal protein catabolic process
N0016020cellular_componentmembrane
N0042802molecular_functionidentical protein binding
N0043068biological_processpositive regulation of programmed cell death
N0051117molecular_functionATPase binding
Functional Information from PDB Data
site_idAC1
Number of Residues15
Detailsbinding site for residue KHS A 301
ChainResidue
AARG36
GLEU62
GPHE63
GALA66
GTHR93
GPHE96
GILE97
ALEU37
AGLU40
AVAL42
ATYR74
ATYR76
APHE126
ALEU128
AARG206

site_idAC2
Number of Residues5
Detailsbinding site for residue GOL A 302
ChainResidue
AGLU155
ALYS158
AVAL159
BARG132
BSER189

site_idAC3
Number of Residues15
Detailsbinding site for residue KHS B 301
ChainResidue
ALEU62
APHE63
AALA66
ATHR93
APHE96
AILE97
BARG36
BLEU37
BGLU40
BVAL42
BTYR74
BTYR76
BPHE126
BLEU128
BARG206

site_idAC4
Number of Residues6
Detailsbinding site for residue GOL B 302
ChainResidue
BGLU155
BLYS158
BARG162
CARG132
CLEU188
CSER189

site_idAC5
Number of Residues12
Detailsbinding site for residue KHS C 301
ChainResidue
BLEU62
BPHE63
BALA66
BTHR93
BPHE96
CGLU40
CVAL42
CTYR74
CTYR76
CPHE126
CLEU128
CARG206

site_idAC6
Number of Residues7
Detailsbinding site for residue GOL C 302
ChainResidue
CGLU155
CLYS158
CVAL159
DARG132
DPHE187
DSER189
DHOH406

site_idAC7
Number of Residues14
Detailsbinding site for residue KHS D 301
ChainResidue
CLEU62
CPHE63
CALA66
CTHR93
CPHE96
DARG36
DLEU37
DGLU40
DVAL42
DTYR74
DTYR76
DPHE126
DLEU128
DARG206

site_idAC8
Number of Residues6
Detailsbinding site for residue GOL D 302
ChainResidue
DGLU155
DLYS158
DVAL159
EARG132
ESER189
EHOH443

site_idAC9
Number of Residues14
Detailsbinding site for residue KHS E 301
ChainResidue
DLEU62
DPHE63
DALA66
DTHR93
DPHE96
EARG36
ELEU37
EGLU40
EVAL42
ETYR74
ETYR76
EPHE126
ELEU128
EARG206

site_idAD1
Number of Residues4
Detailsbinding site for residue GOL E 302
ChainResidue
EGLU155
ELYS158
FARG132
FSER189

site_idAD2
Number of Residues15
Detailsbinding site for residue KHS F 301
ChainResidue
EPHE63
EALA66
ETHR93
EPHE96
EILE97
FARG36
FLEU37
FGLU40
FVAL42
FTYR74
FTYR76
FPHE126
FLEU128
FARG206
ELEU62

site_idAD3
Number of Residues6
Detailsbinding site for residue GOL F 302
ChainResidue
FGLU155
FLYS158
FVAL159
GARG132
GSER189
GHOH422

site_idAD4
Number of Residues15
Detailsbinding site for residue KHS G 301
ChainResidue
FLEU62
FPHE63
FALA66
FTHR93
FPHE96
FILE97
GARG36
GGLU40
GVAL42
GTYR74
GTYR76
GPHE126
GLEU128
GARG206
GHOH476

site_idAD5
Number of Residues4
Detailsbinding site for residue GOL G 302
ChainResidue
AARG132
ASER189
GGLU155
GARG162

site_idAD6
Number of Residues15
Detailsbinding site for residue KHS H 301
ChainResidue
HARG36
HLEU37
HGLU40
HVAL42
HTYR74
HTYR76
HPHE126
HLEU128
HARG206
HHOH442
ILEU62
IPHE63
IALA66
ITHR93
IPHE96

site_idAD7
Number of Residues6
Detailsbinding site for residue GOL H 302
ChainResidue
HGLU155
HLYS158
HARG162
NARG132
NLEU188
NSER189

site_idAD8
Number of Residues15
Detailsbinding site for residue KHS I 301
ChainResidue
IARG36
ILEU37
IGLU40
IVAL42
ITYR74
ITYR76
IPHE126
ILEU128
IARG206
IHOH452
JLEU62
JPHE63
JALA66
JTHR93
JPHE96

site_idAD9
Number of Residues5
Detailsbinding site for residue GOL I 302
ChainResidue
HARG132
HSER189
IGLU155
ILYS158
IVAL159

site_idAE1
Number of Residues15
Detailsbinding site for residue KHS J 301
ChainResidue
JARG36
JLEU37
JGLU40
JVAL42
JTYR74
JTYR76
JPHE126
JLEU128
JARG206
KLEU62
KPHE63
KALA66
KTHR93
KPHE96
KILE97

site_idAE2
Number of Residues4
Detailsbinding site for residue GOL J 302
ChainResidue
IARG132
ISER189
JGLU155
JLYS158

site_idAE3
Number of Residues14
Detailsbinding site for residue KHS K 301
ChainResidue
KARG36
KGLU40
KVAL42
KTYR74
KTYR76
KMET106
KPHE126
KLEU128
KARG206
LLEU62
LPHE63
LALA66
LTHR93
LPHE96

site_idAE4
Number of Residues7
Detailsbinding site for residue GOL K 302
ChainResidue
JARG132
JSER189
KGLU155
KLYS158
KVAL159
KHOH413
KHOH447

site_idAE5
Number of Residues14
Detailsbinding site for residue KHS L 301
ChainResidue
LARG36
LLEU37
LGLU40
LVAL42
LTYR74
LTYR76
LPHE126
LLEU128
LARG206
MLEU62
MPHE63
MALA66
MTHR93
MPHE96

site_idAE6
Number of Residues5
Detailsbinding site for residue GOL L 302
ChainResidue
KARG132
KSER189
KHOH434
LGLU155
LLYS158

site_idAE7
Number of Residues14
Detailsbinding site for residue KHS M 301
ChainResidue
EGLU70
MARG36
MLEU37
MGLU40
MVAL42
MTYR74
MTYR76
MPHE126
MLEU128
MARG206
NLEU62
NALA66
NTHR93
NPHE96

site_idAE8
Number of Residues6
Detailsbinding site for residue GOL M 302
ChainResidue
LARG132
LLEU188
LSER189
MGLU155
MLYS158
MVAL159

site_idAE9
Number of Residues15
Detailsbinding site for residue KHS N 301
ChainResidue
HLEU62
HPHE63
HALA66
HTHR93
HPHE96
HILE97
NARG36
NLEU37
NGLU40
NVAL42
NTYR74
NTYR76
NPHE126
NLEU128
NARG206

site_idAF1
Number of Residues6
Detailsbinding site for residue GOL N 302
ChainResidue
MARG132
MLEU188
MSER189
NGLU155
NLYS158
NHOH414

Functional Information from PROSITE/UniProt
site_idPS00381
Number of Residues12
DetailsCLP_PROTEASE_SER Endopeptidase Clp serine active site. TicMGqAASMGA
ChainResidueDetails
ATHR103-ALA114

site_idPS00382
Number of Residues14
DetailsCLP_PROTEASE_HIS Endopeptidase Clp histidine active site. RfclPnsrVMIHQP
ChainResidueDetails
AARG125-PRO138

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues14
DetailsACT_SITE: Nucleophile => ECO:0000305
ChainResidueDetails
ASER111
BSER111
CSER111
DSER111
ESER111
FSER111
GSER111
HSER111
ISER111
JSER111
KSER111
LSER111
MSER111
NSER111

site_idSWS_FT_FI2
Number of Residues28
DetailsACT_SITE: ACT_SITE => ECO:0000305
ChainResidueDetails
AHIS136
AASP185
BHIS136
BASP185
CHIS136
CASP185
DHIS136
DASP185
EHIS136
EASP185
FHIS136
FASP185
GHIS136
GASP185
HHIS136
HASP185
IHIS136
IASP185
JHIS136
JASP185
KHIS136
KASP185
LHIS136
LASP185
MHIS136
MASP185
NHIS136
NASP185

Catalytic Information from CSA
site_idMCSA1
Number of Residues5
DetailsM-CSA 912
ChainResidueDetails
AGLY82electrostatic stabiliser
ASER111covalent catalysis, proton shuttle (general acid/base)
AMET112electrostatic stabiliser
AHIS136proton shuttle (general acid/base)
AASP185electrostatic stabiliser, modifies pKa

site_idMCSA2
Number of Residues5
DetailsM-CSA 912
ChainResidueDetails
BGLY82electrostatic stabiliser
BSER111covalent catalysis, proton shuttle (general acid/base)
BMET112electrostatic stabiliser
BHIS136proton shuttle (general acid/base)
BASP185electrostatic stabiliser, modifies pKa

site_idMCSA3
Number of Residues5
DetailsM-CSA 912
ChainResidueDetails
CGLY82electrostatic stabiliser
CSER111covalent catalysis, proton shuttle (general acid/base)
CMET112electrostatic stabiliser
CHIS136proton shuttle (general acid/base)
CASP185electrostatic stabiliser, modifies pKa

site_idMCSA4
Number of Residues5
DetailsM-CSA 912
ChainResidueDetails
DGLY82electrostatic stabiliser
DSER111covalent catalysis, proton shuttle (general acid/base)
DMET112electrostatic stabiliser
DHIS136proton shuttle (general acid/base)
DASP185electrostatic stabiliser, modifies pKa

site_idMCSA5
Number of Residues5
DetailsM-CSA 912
ChainResidueDetails
EGLY82electrostatic stabiliser
ESER111covalent catalysis, proton shuttle (general acid/base)
EMET112electrostatic stabiliser
EHIS136proton shuttle (general acid/base)
EASP185electrostatic stabiliser, modifies pKa

site_idMCSA6
Number of Residues5
DetailsM-CSA 912
ChainResidueDetails
FGLY82electrostatic stabiliser
FSER111covalent catalysis, proton shuttle (general acid/base)
FMET112electrostatic stabiliser
FHIS136proton shuttle (general acid/base)
FASP185electrostatic stabiliser, modifies pKa

site_idMCSA7
Number of Residues5
DetailsM-CSA 912
ChainResidueDetails
GGLY82electrostatic stabiliser
GSER111covalent catalysis, proton shuttle (general acid/base)
GMET112electrostatic stabiliser
GHIS136proton shuttle (general acid/base)
GASP185electrostatic stabiliser, modifies pKa

site_idMCSA8
Number of Residues5
DetailsM-CSA 912
ChainResidueDetails
HGLY82electrostatic stabiliser
HSER111covalent catalysis, proton shuttle (general acid/base)
HMET112electrostatic stabiliser
HHIS136proton shuttle (general acid/base)
HASP185electrostatic stabiliser, modifies pKa

site_idMCSA9
Number of Residues5
DetailsM-CSA 912
ChainResidueDetails
IGLY82electrostatic stabiliser
ISER111covalent catalysis, proton shuttle (general acid/base)
IMET112electrostatic stabiliser
IHIS136proton shuttle (general acid/base)
IASP185electrostatic stabiliser, modifies pKa

site_idMCSA10
Number of Residues5
DetailsM-CSA 912
ChainResidueDetails
JGLY82electrostatic stabiliser
JSER111covalent catalysis, proton shuttle (general acid/base)
JMET112electrostatic stabiliser
JHIS136proton shuttle (general acid/base)
JASP185electrostatic stabiliser, modifies pKa

site_idMCSA11
Number of Residues5
DetailsM-CSA 912
ChainResidueDetails
KGLY82electrostatic stabiliser
KSER111covalent catalysis, proton shuttle (general acid/base)
KMET112electrostatic stabiliser
KHIS136proton shuttle (general acid/base)
KASP185electrostatic stabiliser, modifies pKa

site_idMCSA12
Number of Residues5
DetailsM-CSA 912
ChainResidueDetails
LGLY82electrostatic stabiliser
LSER111covalent catalysis, proton shuttle (general acid/base)
LMET112electrostatic stabiliser
LHIS136proton shuttle (general acid/base)
LASP185electrostatic stabiliser, modifies pKa

site_idMCSA13
Number of Residues5
DetailsM-CSA 912
ChainResidueDetails
MGLY82electrostatic stabiliser
MSER111covalent catalysis, proton shuttle (general acid/base)
MMET112electrostatic stabiliser
MHIS136proton shuttle (general acid/base)
MASP185electrostatic stabiliser, modifies pKa

site_idMCSA14
Number of Residues5
DetailsM-CSA 912
ChainResidueDetails
NGLY82electrostatic stabiliser
NSER111covalent catalysis, proton shuttle (general acid/base)
NMET112electrostatic stabiliser
NHIS136proton shuttle (general acid/base)
NASP185electrostatic stabiliser, modifies pKa

221051

PDB entries from 2024-06-12

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