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1XPO
Biol. Unit 1
Info
Asym.Unit (406 KB)
Biol.Unit 1 (70 KB)
Biol.Unit 2 (71 KB)
Biol.Unit 3 (71 KB)
Biol.Unit 4 (71 KB)
Biol.Unit 5 (71 KB)
Biol.Unit 6 (72 KB)
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(1)
Title
:
STRUCTURAL MECHANISM OF INHIBITION OF THE RHO TRANSCRIPTION TERMINATION FACTOR BY THE ANTIBIOTIC BICYCLOMYCIN
Authors
:
E. Skordalakes, A. P. Brogan, B. S. Park, H. Kohn, J. M. Berger
Date
:
09 Oct 04 (Deposition) - 08 Feb 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.15
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; Bicyclomycin, 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
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Hetero Components
(1, 1)
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: BICYCLOMYCIN (BCMa)
2b: BICYCLOMYCIN (BCMb)
2c: BICYCLOMYCIN (BCMc)
2d: BICYCLOMYCIN (BCMd)
2e: BICYCLOMYCIN (BCMe)
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
1
Ligand/Ion
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
2
BCM
-1
Ligand/Ion
BICYCLOMYCIN
3
MG
-1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC7 (SOFTWARE)
3: AC8 (SOFTWARE)
4: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:185 , ARG A:212 , GLU A:215 , AGS A:1600
BINDING SITE FOR RESIDUE MG A 1601
2
AC7
SOFTWARE
THR A:158 , PRO A:180 , LYS A:181 , ALA A:182 , GLY A:183 , LYS A:184 , THR A:185 , MET A:186 , ARG A:212 , PHE A:355 , MG A:1601
BINDING SITE FOR RESIDUE AGS A 1600
3
AC8
SOFTWARE
ARG A:366 , LYS A:367 , GLU A:369 , PRO B:180 , LYS B:181 , ALA B:182 , GLY B:183 , LYS B:184 , THR B:185 , MET B:186 , ARG B:212 , PHE B:355 , MG B:2601 , BCM B:2701
BINDING SITE FOR RESIDUE AGS B 2600
4
AC9
SOFTWARE
LYS A:336 , GLY A:337 , PRO B:180 , LYS B:184 , ASP B:210 , GLU B:211 , ASP B:265 , SER B:266 , ARG B:269 , LEU B:320 , THR B:323 , AGS B:2600 , MG B:2601
BINDING SITE FOR RESIDUE BCM B 2701
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
Info
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Exons
(0, 0)
Info
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 18)
Info
All SCOP Domains
1a: SCOP_d1xpoa1 (A:1-47)
1b: SCOP_d1xpob1 (B:1-47)
1c: SCOP_d1xpoc1 (C:1-47)
1d: SCOP_d1xpod1 (D:1-47)
1e: SCOP_d1xpoe1 (E:1-47)
1f: SCOP_d1xpof1 (F:1-47)
2a: SCOP_d1xpoa2 (A:48-129)
2b: SCOP_d1xpob2 (B:48-129)
2c: SCOP_d1xpoc2 (C:48-129)
2d: SCOP_d1xpod2 (D:48-129)
2e: SCOP_d1xpoe2 (E:48-129)
2f: SCOP_d1xpof2 (F:48-129)
3a: SCOP_d1xpoa3 (A:130-417)
3b: SCOP_d1xpob3 (B:130-417)
3c: SCOP_d1xpoc3 (C:130-417)
3d: SCOP_d1xpod3 (D:130-417)
3e: SCOP_d1xpoe3 (E:130-417)
3f: SCOP_d1xpof3 (F:130-417)
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Classes
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)
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)
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(
)
(
)
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
d1xpoa1
A:1-47
1b
d1xpob1
B:1-47
1c
d1xpoc1
C:1-47
1d
d1xpod1
D:1-47
1e
d1xpoe1
E:1-47
1f
d1xpof1
F: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
d1xpoa2
A:48-129
2b
d1xpob2
B:48-129
2c
d1xpoc2
C:48-129
2d
d1xpod2
D:48-129
2e
d1xpoe2
E:48-129
2f
d1xpof2
F:48-129
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
d1xpoa3
A:130-417
3b
d1xpob3
B:130-417
3c
d1xpoc3
C:130-417
3d
d1xpod3
D:130-417
3e
d1xpoe3
E:130-417
3f
d1xpof3
F:130-417
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1xpoE02 (E:129-417)
1b: CATH_1xpoA02 (A:129-417)
1c: CATH_1xpoB02 (B:129-417)
1d: CATH_1xpoC02 (C:129-417)
1e: CATH_1xpoD02 (D:129-417)
1f: CATH_1xpoF02 (F:129-417)
2a: CATH_1xpoA01 (A:1-126)
2b: CATH_1xpoB01 (B:1-126)
2c: CATH_1xpoC01 (C:1-126)
2d: CATH_1xpoD01 (D:1-126)
2e: CATH_1xpoE01 (E:1-126)
2f: CATH_1xpoF01 (F:1-126)
View:
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)
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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
1xpoE02
E:129-417
1b
1xpoA02
A:129-417
1c
1xpoB02
B:129-417
1d
1xpoC02
C:129-417
1e
1xpoD02
D:129-417
1f
1xpoF02
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
1xpoA01
A:1-126
2b
1xpoB01
B:1-126
2c
1xpoC01
C:1-126
2d
1xpoD01
D:1-126
2e
1xpoE01
E:1-126
2f
1xpoF01
F:1-126
[
close CATH info
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Pfam Domains
(3, 18)
Info
all PFAM domains
1a: PFAM_Rho_N_1xpoF01 (F:5-47)
1b: PFAM_Rho_N_1xpoF02 (F:5-47)
1c: PFAM_Rho_N_1xpoF03 (F:5-47)
1d: PFAM_Rho_N_1xpoF04 (F:5-47)
1e: PFAM_Rho_N_1xpoF05 (F:5-47)
1f: PFAM_Rho_N_1xpoF06 (F:5-47)
2a: PFAM_Rho_RNA_bind_1xpoF07 (F:49-126)
2b: PFAM_Rho_RNA_bind_1xpoF08 (F:49-126)
2c: PFAM_Rho_RNA_bind_1xpoF09 (F:49-126)
2d: PFAM_Rho_RNA_bind_1xpoF10 (F:49-126)
2e: PFAM_Rho_RNA_bind_1xpoF11 (F:49-126)
2f: PFAM_Rho_RNA_bind_1xpoF12 (F:49-126)
3a: PFAM_ATP_synt_ab_1xpoF13 (F:157-365)
3b: PFAM_ATP_synt_ab_1xpoF14 (F:157-365)
3c: PFAM_ATP_synt_ab_1xpoF15 (F:157-365)
3d: PFAM_ATP_synt_ab_1xpoF16 (F:157-365)
3e: PFAM_ATP_synt_ab_1xpoF17 (F:157-365)
3f: PFAM_ATP_synt_ab_1xpoF18 (F:157-365)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HeH
(20)
Family
:
Rho_N
(5)
Escherichia coli (strain K12)
(5)
1a
Rho_N-1xpoF01
F:5-47
1b
Rho_N-1xpoF02
F:5-47
1c
Rho_N-1xpoF03
F:5-47
1d
Rho_N-1xpoF04
F:5-47
1e
Rho_N-1xpoF05
F:5-47
1f
Rho_N-1xpoF06
F:5-47
Clan
:
OB
(224)
Family
:
Rho_RNA_bind
(5)
Escherichia coli (strain K12)
(5)
2a
Rho_RNA_bind-1xpoF07
F:49-126
2b
Rho_RNA_bind-1xpoF08
F:49-126
2c
Rho_RNA_bind-1xpoF09
F:49-126
2d
Rho_RNA_bind-1xpoF10
F:49-126
2e
Rho_RNA_bind-1xpoF11
F:49-126
2f
Rho_RNA_bind-1xpoF12
F:49-126
Clan
:
P-loop_NTPase
(1112)
Family
:
ATP-synt_ab
(44)
Escherichia coli (strain K12)
(5)
3a
ATP-synt_ab-1xpoF13
F:157-365
3b
ATP-synt_ab-1xpoF14
F:157-365
3c
ATP-synt_ab-1xpoF15
F:157-365
3d
ATP-synt_ab-1xpoF16
F:157-365
3e
ATP-synt_ab-1xpoF17
F:157-365
3f
ATP-synt_ab-1xpoF18
F:157-365
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Asym.Unit (406 KB)
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