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3KTI
Asym. Unit
Info
Asym.Unit (219 KB)
Biol.Unit 1 (211 KB)
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(1)
Title
:
STRUCTURE OF CLPP IN COMPLEX WITH ADEP1
Authors
:
B. -G. Lee, H. Brotz-Oesterhelt, H. K. Song
Date
:
25 Nov 09 (Deposition) - 23 Mar 10 (Release) - 10 Nov 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N (1x)
Keywords
:
Hydrolase, Protease, Serine Protease, Stress Response, A54556A, Enopeptin, Depsipeptide, Antibiotics, Hydrolase-Antibiotic Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. -G. Lee, E. Y. Park, K. -E. Lee, H. Jeon, K. H. Sung, H. Paulsen, H. Rubsamen-Schaeff, H. Brotz-Oesterhelt, H. K. Song
Structures Of Clpp In Complex With Acyldepsipeptide Antibiotics Reveal Its Activation Mechanism
Nat. Struct. Mol. Biol. V. 17 471 2010
[
close entry info
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Hetero Components
(5, 35)
Info
All Hetero Components
1a: DIMETHYL SULFOXIDE (DMSa)
1b: DIMETHYL SULFOXIDE (DMSb)
1c: DIMETHYL SULFOXIDE (DMSc)
1d: DIMETHYL SULFOXIDE (DMSd)
1e: DIMETHYL SULFOXIDE (DMSe)
1f: DIMETHYL SULFOXIDE (DMSf)
1g: DIMETHYL SULFOXIDE (DMSg)
2a: N-METHYL-L-ALANINE (MAAa)
2b: N-METHYL-L-ALANINE (MAAb)
2c: N-METHYL-L-ALANINE (MAAc)
2d: N-METHYL-L-ALANINE (MAAd)
2e: N-METHYL-L-ALANINE (MAAe)
2f: N-METHYL-L-ALANINE (MAAf)
2g: N-METHYL-L-ALANINE (MAAg)
3a: (4R)-4-METHYL-L-PROLINE (MP8a)
3b: (4R)-4-METHYL-L-PROLINE (MP8b)
3c: (4R)-4-METHYL-L-PROLINE (MP8c)
3d: (4R)-4-METHYL-L-PROLINE (MP8d)
3e: (4R)-4-METHYL-L-PROLINE (MP8e)
3f: (4R)-4-METHYL-L-PROLINE (MP8f)
3g: (4R)-4-METHYL-L-PROLINE (MP8g)
4a: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFON... (NHEa)
4b: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFON... (NHEb)
4c: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFON... (NHEc)
4d: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFON... (NHEd)
4e: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFON... (NHEe)
4f: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFON... (NHEf)
4g: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFON... (NHEg)
5a: (2E,4E,6E)-OCTA-2,4,6-TRIENOIC ACI... (OTTa)
5b: (2E,4E,6E)-OCTA-2,4,6-TRIENOIC ACI... (OTTb)
5c: (2E,4E,6E)-OCTA-2,4,6-TRIENOIC ACI... (OTTc)
5d: (2E,4E,6E)-OCTA-2,4,6-TRIENOIC ACI... (OTTd)
5e: (2E,4E,6E)-OCTA-2,4,6-TRIENOIC ACI... (OTTe)
5f: (2E,4E,6E)-OCTA-2,4,6-TRIENOIC ACI... (OTTf)
5g: (2E,4E,6E)-OCTA-2,4,6-TRIENOIC ACI... (OTTg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DMS
7
Ligand/Ion
DIMETHYL SULFOXIDE
2
MAA
7
Mod. Amino Acid
N-METHYL-L-ALANINE
3
MP8
7
Mod. Amino Acid
(4R)-4-METHYL-L-PROLINE
4
NHE
7
Ligand/Ion
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
5
OTT
7
Mod. Amino Acid
(2E,4E,6E)-OCTA-2,4,6-TRIENOIC ACID
[
close Hetero Component info
]
Sites
(21, 21)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:97 , ILE A:121 , HIS A:122 , LEU A:153
BINDING SITE FOR RESIDUE DMS A 301
02
AC2
SOFTWARE
SER A:69 , ILE A:70 , THR A:71 , ARG A:141 , HOH A:238 , HOH A:612 , MET B:94
BINDING SITE FOR RESIDUE NHE A 501
03
AC3
SOFTWARE
ILE B:121 , HIS B:122 , LEU B:153
BINDING SITE FOR RESIDUE DMS B 302
04
AC4
SOFTWARE
ILE B:70 , THR B:71 , ARG B:141 , HOH B:403 , HOH B:517 , PRO C:66 , MET C:94
BINDING SITE FOR RESIDUE NHE B 502
05
AC5
SOFTWARE
ILE C:121 , HIS C:122 , LEU C:153
BINDING SITE FOR RESIDUE DMS C 303
06
AC6
SOFTWARE
SER C:69 , ILE C:70 , THR C:71 , ARG C:141 , HOH C:214 , HOH C:663 , PRO D:66
BINDING SITE FOR RESIDUE NHE C 503
07
AC7
SOFTWARE
SER D:97 , ILE D:121 , HIS D:122 , LEU D:153
BINDING SITE FOR RESIDUE DMS D 304
08
AC8
SOFTWARE
ILE D:70 , THR D:71 , ARG D:141 , HOH D:400 , PRO E:66 , MET E:94
BINDING SITE FOR RESIDUE NHE D 504
09
AC9
SOFTWARE
ILE E:121 , HIS E:122
BINDING SITE FOR RESIDUE DMS E 305
10
BC1
SOFTWARE
SER E:69 , ILE E:70 , THR E:71 , ARG E:141 , HOH E:409
BINDING SITE FOR RESIDUE NHE E 505
11
BC2
SOFTWARE
SER F:97 , ILE F:121 , HIS F:122
BINDING SITE FOR RESIDUE DMS F 306
12
BC3
SOFTWARE
SER F:69 , ILE F:70 , THR F:71 , ARG F:141 , LEU F:145 , HOH F:394 , HOH F:492 , PRO G:66 , MET G:94
BINDING SITE FOR RESIDUE NHE F 506
13
BC4
SOFTWARE
ILE G:121 , HIS G:122
BINDING SITE FOR RESIDUE DMS G 307
14
BC5
SOFTWARE
PRO A:66 , SER G:69 , ILE G:70 , THR G:71 , ARG G:141
BINDING SITE FOR RESIDUE NHE G 507
15
BC6
SOFTWARE
ALA A:52 , THR A:79 , PHE A:82 , HOH A:485 , ARG B:22 , ASP B:26 , SER B:60 , TYR B:62 , ILE B:90 , ILE B:92 , LYS B:110 , TYR B:112 , LEU B:189
BINDING SITE FOR CHAIN H OF ACYLDEPSIPEPTIDE 1
16
BC7
SOFTWARE
ARG A:22 , ASP A:26 , GLU A:58 , SER A:60 , TYR A:62 , ILE A:90 , ILE A:92 , LYS A:110 , TYR A:112 , LEU A:114 , LEU A:189 , LEU G:48 , ALA G:52 , THR G:79 , PHE G:82
BINDING SITE FOR CHAIN I OF ACYLDEPSIPEPTIDE 1
17
BC8
SOFTWARE
THR E:79 , PHE E:82 , ASP F:26 , SER F:60 , TYR F:62 , ILE F:90 , LYS F:110 , TYR F:112 , LEU F:114 , LEU F:189
BINDING SITE FOR CHAIN J OF ACYLDEPSIPEPTIDE 1
18
BC9
SOFTWARE
ALA B:52 , THR B:79 , PHE B:82 , ARG C:22 , ASP C:26 , GLU C:58 , SER C:60 , TYR C:62 , ILE C:90 , LYS C:110 , TYR C:112 , LEU C:189
BINDING SITE FOR CHAIN K OF ACYLDEPSIPEPTIDE 1
19
CC1
SOFTWARE
THR C:79 , PHE C:82 , ARG D:22 , ASP D:26 , ILE D:28 , GLU D:58 , SER D:60 , TYR D:62 , ILE D:90 , ILE D:92 , TYR D:112 , LEU D:189 , HOH D:410
BINDING SITE FOR CHAIN L OF ACYLDEPSIPEPTIDE 1
20
CC2
SOFTWARE
THR D:79 , PHE D:82 , HOH D:236 , ARG E:22 , LEU E:23 , ASP E:26 , SER E:60 , TYR E:62 , ILE E:90 , ILE E:92 , LYS E:110 , TYR E:112 , LEU E:114 , LEU E:189
BINDING SITE FOR CHAIN M OF ACYLDEPSIPEPTIDE 1
21
CC3
SOFTWARE
LEU F:48 , THR F:79 , PHE F:82 , HOH F:238 , ARG G:22 , ASP G:26 , ILE G:28 , SER G:60 , TYR G:62 , ILE G:90 , TYR G:112 , LEU G:114 , LEU G:189 , HOH N:420 , HOH N:561
BINDING SITE FOR CHAIN N OF ACYLDEPSIPEPTIDE 1
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(2, 14)
Info
All PROSITE Patterns/Profiles
1: CLP_PROTEASE_SER (A:89-100,B:89-100,C:89-100,D:89-10...)
2: CLP_PROTEASE_HIS (A:111-124,B:111-124,C:111-124,D:11...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CLP_PROTEASE_SER
PS00381
Endopeptidase Clp serine active site.
CLPP_BACSU
90-101
7
A:89-100
B:89-100
C:89-100
D:89-100
E:89-100
F:89-100
G:89-100
2
CLP_PROTEASE_HIS
PS00382
Endopeptidase Clp histidine active site.
CLPP_BACSU
112-125
7
A:111-124
B:111-124
C:111-124
D:111-124
E:111-124
F:111-124
G:111-124
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 7)
Info
All SCOP Domains
1a: SCOP_d3ktia_ (A:)
1b: SCOP_d3ktib_ (B:)
1c: SCOP_d3ktic_ (C:)
1d: SCOP_d3ktid_ (D:)
1e: SCOP_d3ktie_ (E:)
1f: SCOP_d3ktif_ (F:)
1g: SCOP_d3ktig_ (G:)
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)
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)
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(
)
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)
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)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
ClpP/crotonase
(207)
Superfamily
:
ClpP/crotonase
(207)
Family
:
Clp protease, ClpP subunit
(31)
Protein domain
:
automated matches
(16)
Bacillus subtilis [TaxId: 1423]
(5)
1a
d3ktia_
A:
1b
d3ktib_
B:
1c
d3ktic_
C:
1d
d3ktid_
D:
1e
d3ktie_
E:
1f
d3ktif_
F:
1g
d3ktig_
G:
[
close SCOP info
]
CATH Domains
(1, 7)
Info
all CATH domains
1a: CATH_3ktiA00 (A:18-191)
1b: CATH_3ktiB00 (B:18-191)
1c: CATH_3ktiC00 (C:18-191)
1d: CATH_3ktiD00 (D:18-191)
1e: CATH_3ktiE00 (E:18-191)
1f: CATH_3ktiF00 (F:18-191)
1g: CATH_3ktiG00 (G:18-191)
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Classes
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)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
2-enoyl-CoA Hydratase; Chain A, domain 1
(89)
Homologous Superfamily
:
2-enoyl-CoA Hydratase; Chain A, domain 1
(89)
Bacillus subtilis. Organism_taxid: 1423.
(5)
1a
3ktiA00
A:18-191
1b
3ktiB00
B:18-191
1c
3ktiC00
C:18-191
1d
3ktiD00
D:18-191
1e
3ktiE00
E:18-191
1f
3ktiF00
F:18-191
1g
3ktiG00
G:18-191
[
close CATH info
]
Pfam Domains
(1, 7)
Info
all PFAM domains
1a: PFAM_CLP_protease_3ktiG01 (G:18-191)
1b: PFAM_CLP_protease_3ktiG02 (G:18-191)
1c: PFAM_CLP_protease_3ktiG03 (G:18-191)
1d: PFAM_CLP_protease_3ktiG04 (G:18-191)
1e: PFAM_CLP_protease_3ktiG05 (G:18-191)
1f: PFAM_CLP_protease_3ktiG06 (G:18-191)
1g: PFAM_CLP_protease_3ktiG07 (G:18-191)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
ClpP_crotonase
(88)
Family
:
CLP_protease
(18)
Bacillus subtilis
(5)
1a
CLP_protease-3ktiG01
G:18-191
1b
CLP_protease-3ktiG02
G:18-191
1c
CLP_protease-3ktiG03
G:18-191
1d
CLP_protease-3ktiG04
G:18-191
1e
CLP_protease-3ktiG05
G:18-191
1f
CLP_protease-3ktiG06
G:18-191
1g
CLP_protease-3ktiG07
G:18-191
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