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1XPU
Asym. Unit
Info
Asym.Unit (364 KB)
Biol.Unit 1 (64 KB)
Biol.Unit 2 (64 KB)
Biol.Unit 3 (64 KB)
Biol.Unit 4 (64 KB)
Biol.Unit 5 (65 KB)
Biol.Unit 6 (64 KB)
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(1)
Title
:
STRUCTURAL MECHANISM OF INHIBITION OF THE RHO TRANSCRIPTION TERMINATION FACTOR BY THE ANTIBIOTIC 5A-(3-FORMYLPHENYLSULFANYL)-DIHYDROBICYCLOMYCIN (FPDB)
Authors
:
E. Skordalakes, A. P. Brogan, B. S. Park, H. Kohn, J. M. Berger
Date
:
09 Oct 04 (Deposition) - 02 Nov 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.05
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,J,K,L,M
Biol. Unit 1: A,G (1x)
Biol. Unit 2: B,M (1x)
Biol. Unit 3: C,H (1x)
Biol. Unit 4: D,J (1x)
Biol. Unit 5: E,K (1x)
Biol. Unit 6: F,L (1x)
Keywords
:
Rho Transcription Termination Factor; 5A-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb); Atpgammas, Transcription-Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Skordalakes, A. P. Brogan, B. S. Park, H. Kohn, J. M. Berger
Structural Mechanism Of Inhibition Of The Rho Transcription Termination Factor By The Antibiotic Bicyclomycin
Structure V. 13 99 2005
[
close entry info
]
Hetero Components
(3, 17)
Info
All Hetero Components
1a: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLA... (AGSa)
1b: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLA... (AGSb)
1c: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLA... (AGSc)
1d: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLA... (AGSd)
1e: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLA... (AGSe)
1f: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLA... (AGSf)
2a: 5A-(3-FORMYLPHENYLSULFANYL)-DIHYDR... (FPDa)
2b: 5A-(3-FORMYLPHENYLSULFANYL)-DIHYDR... (FPDb)
2c: 5A-(3-FORMYLPHENYLSULFANYL)-DIHYDR... (FPDc)
2d: 5A-(3-FORMYLPHENYLSULFANYL)-DIHYDR... (FPDd)
2e: 5A-(3-FORMYLPHENYLSULFANYL)-DIHYDR... (FPDe)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AGS
6
Ligand/Ion
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
2
FPD
5
Ligand/Ion
5A-(3-FORMYLPHENYLSULFANYL)-DIHYDROBICYCLOMYCIN
3
MG
6
Ligand/Ion
MAGNESIUM ION
[
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]
Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:184 , THR A:185 , GLU A:215 , AGS A:1600
BINDING SITE FOR RESIDUE MG A 1601
02
AC2
SOFTWARE
LYS B:184 , THR B:185 , AGS B:2600 , FPD B:2701 , HOH B:2702
BINDING SITE FOR RESIDUE MG B 2601
03
AC3
SOFTWARE
LYS C:184 , THR C:185 , ASP C:265 , AGS C:3600
BINDING SITE FOR RESIDUE MG C 3601
04
AC4
SOFTWARE
THR D:185 , ARG D:212 , AGS D:4600
BINDING SITE FOR RESIDUE MG D 4601
05
AC5
SOFTWARE
LYS E:184 , THR E:185 , GLU E:211 , GLU E:215 , AGS E:5600
BINDING SITE FOR RESIDUE MG E 5601
06
AC6
SOFTWARE
AGS E:6600 , LYS F:184 , THR F:185 , FPD F:6701
BINDING SITE FOR RESIDUE MG F 6601
07
AC7
SOFTWARE
THR A:158 , LYS A:181 , ALA A:182 , GLY A:183 , LYS A:184 , THR A:185 , MET A:186 , PHE A:355 , MG A:1601
BINDING SITE FOR RESIDUE AGS A 1600
08
AC8
SOFTWARE
ARG A:366 , THR B:158 , PRO B:180 , LYS B:181 , ALA B:182 , GLY B:183 , LYS B:184 , THR B:185 , MET B:186 , PHE B:355 , MG B:2601 , HOH B:2702
BINDING SITE FOR RESIDUE AGS B 2600
09
AC9
SOFTWARE
LYS A:336 , GLY A:337 , GLU A:342 , ARG A:366 , PRO B:180 , LYS B:181 , LYS B:184 , ASP B:210 , GLU B:211 , ARG B:212 , ASP B:265 , SER B:266 , ARG B:269 , LEU B:320 , THR B:323 , MG B:2601
BINDING SITE FOR RESIDUE FPD B 2701
10
BC1
SOFTWARE
ARG B:366 , THR C:158 , LYS C:181 , ALA C:182 , GLY C:183 , LYS C:184 , THR C:185 , MET C:186 , ARG C:212 , PHE C:355 , MG C:3601
BINDING SITE FOR RESIDUE AGS C 3600
11
BC2
SOFTWARE
LYS B:336 , GLY B:337 , GLU B:342 , ARG B:366 , LYS C:181 , LYS C:184 , ASP C:210 , GLU C:211 , ARG C:212 , ASP C:265 , SER C:266 , ARG C:269 , LEU C:320 , THR C:323
BINDING SITE FOR RESIDUE FPD C 3701
12
BC3
SOFTWARE
ARG C:366 , THR D:158 , LYS D:181 , ALA D:182 , GLY D:183 , LYS D:184 , THR D:185 , MET D:186 , ARG D:212 , PHE D:355 , MG D:4601 , FPD D:4701
BINDING SITE FOR RESIDUE AGS D 4600
13
BC4
SOFTWARE
LYS C:336 , GLY C:337 , GLU C:342 , ARG C:366 , LYS D:181 , LYS D:184 , ILE D:209 , ASP D:210 , GLU D:211 , ARG D:212 , ASP D:265 , SER D:266 , ARG D:269 , LEU D:320 , THR D:323 , AGS D:4600
BINDING SITE FOR RESIDUE FPD D 4701
14
BC5
SOFTWARE
ARG D:366 , THR E:158 , LYS E:181 , ALA E:182 , GLY E:183 , LYS E:184 , THR E:185 , MET E:186 , ARG E:353 , PHE E:355 , MG E:5601 , FPD E:5701
BINDING SITE FOR RESIDUE AGS E 5600
15
BC6
SOFTWARE
GLY D:337 , GLU D:342 , ARG D:366 , PRO E:180 , LYS E:181 , LYS E:184 , ASP E:210 , GLU E:211 , ARG E:212 , ASP E:265 , SER E:266 , ARG E:269 , LEU E:320 , THR E:323 , AGS E:5600
BINDING SITE FOR RESIDUE FPD E 5701
16
BC7
SOFTWARE
ARG E:366 , THR F:158 , LYS F:181 , ALA F:182 , GLY F:183 , LYS F:184 , THR F:185 , MET F:186 , PHE F:355 , MG F:6601 , FPD F:6701
BINDING SITE FOR RESIDUE AGS E 6600
17
BC8
SOFTWARE
GLY E:337 , GLU E:342 , AGS E:6600 , PRO F:180 , LYS F:181 , LYS F:184 , ILE F:209 , GLU F:211 , ASP F:265 , SER F:266 , ARG F:269 , LEU F:320 , MG F:6601
BINDING SITE FOR RESIDUE FPD F 6701
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
View:
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End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 18)
Info
All SCOP Domains
1a: SCOP_d1xpua1 (A:1-47)
1b: SCOP_d1xpue1 (E:1-47)
1c: SCOP_d1xpuf1 (F:1-47)
1d: SCOP_d1xpub1 (B:1-47)
1e: SCOP_d1xpuc1 (C:1-47)
1f: SCOP_d1xpud1 (D:1-47)
2a: SCOP_d1xpua2 (A:48-126)
2b: SCOP_d1xpue2 (E:48-126)
2c: SCOP_d1xpuf2 (F:48-126)
2d: SCOP_d1xpub2 (B:48-126)
2e: SCOP_d1xpuc2 (C:48-126)
2f: SCOP_d1xpud2 (D:48-126)
3a: SCOP_d1xpua3 (A:129-417)
3b: SCOP_d1xpub3 (B:129-417)
3c: SCOP_d1xpuc3 (C:129-417)
3d: SCOP_d1xpud3 (D:129-417)
3e: SCOP_d1xpue3 (E:129-417)
3f: SCOP_d1xpuf3 (F:129-417)
View:
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Classes
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)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
LEM/SAP HeH motif
(33)
Superfamily
:
Rho N-terminal domain-like
(11)
Family
:
Rho termination factor, N-terminal domain
(9)
Protein domain
:
Rho termination factor, N-terminal domain
(9)
Escherichia coli [TaxId: 562]
(9)
1a
d1xpua1
A:1-47
1b
d1xpue1
E:1-47
1c
d1xpuf1
F:1-47
1d
d1xpub1
B:1-47
1e
d1xpuc1
C:1-47
1f
d1xpud1
D:1-47
Class
:
All beta proteins
(24004)
Fold
:
OB-fold
(1179)
Superfamily
:
Nucleic acid-binding proteins
(590)
Family
:
Cold shock DNA-binding domain-like
(310)
Protein domain
:
Rho termination factor, RNA-binding domain
(9)
Escherichia coli [TaxId: 562]
(9)
2a
d1xpua2
A:48-126
2b
d1xpue2
E:48-126
2c
d1xpuf2
F:48-126
2d
d1xpub2
B:48-126
2e
d1xpuc2
C:48-126
2f
d1xpud2
D:48-126
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
RecA protein-like (ATPase-domain)
(159)
Protein domain
:
Transcription termination factor Rho, ATPase domain
(5)
Escherichia coli [TaxId: 562]
(5)
3a
d1xpua3
A:129-417
3b
d1xpub3
B:129-417
3c
d1xpuc3
C:129-417
3d
d1xpud3
D:129-417
3e
d1xpue3
E:129-417
3f
d1xpuf3
F:129-417
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1xpuE02 (E:129-417)
1b: CATH_1xpuA02 (A:129-417)
1c: CATH_1xpuB02 (B:129-417)
1d: CATH_1xpuC02 (C:129-417)
1e: CATH_1xpuD02 (D:129-417)
1f: CATH_1xpuF02 (F:129-417)
2a: CATH_1xpuA01 (A:1-126)
2b: CATH_1xpuB01 (B:1-126)
2c: CATH_1xpuC01 (C:1-126)
2d: CATH_1xpuD01 (D:1-126)
2e: CATH_1xpuE01 (E:1-126)
2f: CATH_1xpuF01 (F:1-126)
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
[unclassified]
(24)
1a
1xpuE02
E:129-417
1b
1xpuA02
A:129-417
1c
1xpuB02
B:129-417
1d
1xpuC02
C:129-417
1e
1xpuD02
D:129-417
1f
1xpuF02
F:129-417
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
[unclassified]
(49)
2a
1xpuA01
A:1-126
2b
1xpuB01
B:1-126
2c
1xpuC01
C:1-126
2d
1xpuD01
D:1-126
2e
1xpuE01
E:1-126
2f
1xpuF01
F:1-126
[
close CATH info
]
Pfam Domains
(3, 18)
Info
all PFAM domains
1a: PFAM_Rho_N_1xpuF01 (F:5-47)
1b: PFAM_Rho_N_1xpuF02 (F:5-47)
1c: PFAM_Rho_N_1xpuF03 (F:5-47)
1d: PFAM_Rho_N_1xpuF04 (F:5-47)
1e: PFAM_Rho_N_1xpuF05 (F:5-47)
1f: PFAM_Rho_N_1xpuF06 (F:5-47)
2a: PFAM_Rho_RNA_bind_1xpuF07 (F:49-126)
2b: PFAM_Rho_RNA_bind_1xpuF08 (F:49-126)
2c: PFAM_Rho_RNA_bind_1xpuF09 (F:49-126)
2d: PFAM_Rho_RNA_bind_1xpuF10 (F:49-126)
2e: PFAM_Rho_RNA_bind_1xpuF11 (F:49-126)
2f: PFAM_Rho_RNA_bind_1xpuF12 (F:49-126)
3a: PFAM_ATP_synt_ab_1xpuF13 (F:157-365)
3b: PFAM_ATP_synt_ab_1xpuF14 (F:157-365)
3c: PFAM_ATP_synt_ab_1xpuF15 (F:157-365)
3d: PFAM_ATP_synt_ab_1xpuF16 (F:157-365)
3e: PFAM_ATP_synt_ab_1xpuF17 (F:157-365)
3f: PFAM_ATP_synt_ab_1xpuF18 (F:157-365)
View:
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Clans
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Families
(
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(
)
Organisms
(
)
(
)
Clan
:
HeH
(20)
Family
:
Rho_N
(5)
Escherichia coli (strain K12)
(5)
1a
Rho_N-1xpuF01
F:5-47
1b
Rho_N-1xpuF02
F:5-47
1c
Rho_N-1xpuF03
F:5-47
1d
Rho_N-1xpuF04
F:5-47
1e
Rho_N-1xpuF05
F:5-47
1f
Rho_N-1xpuF06
F:5-47
Clan
:
OB
(224)
Family
:
Rho_RNA_bind
(5)
Escherichia coli (strain K12)
(5)
2a
Rho_RNA_bind-1xpuF07
F:49-126
2b
Rho_RNA_bind-1xpuF08
F:49-126
2c
Rho_RNA_bind-1xpuF09
F:49-126
2d
Rho_RNA_bind-1xpuF10
F:49-126
2e
Rho_RNA_bind-1xpuF11
F:49-126
2f
Rho_RNA_bind-1xpuF12
F:49-126
Clan
:
P-loop_NTPase
(1112)
Family
:
ATP-synt_ab
(44)
Escherichia coli (strain K12)
(5)
3a
ATP-synt_ab-1xpuF13
F:157-365
3b
ATP-synt_ab-1xpuF14
F:157-365
3c
ATP-synt_ab-1xpuF15
F:157-365
3d
ATP-synt_ab-1xpuF16
F:157-365
3e
ATP-synt_ab-1xpuF17
F:157-365
3f
ATP-synt_ab-1xpuF18
F:157-365
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