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1XPR
Biol. Unit 6
Info
Asym.Unit (405 KB)
Biol.Unit 1 (70 KB)
Biol.Unit 2 (71 KB)
Biol.Unit 3 (70 KB)
Biol.Unit 4 (71 KB)
Biol.Unit 5 (71 KB)
Biol.Unit 6 (71 KB)
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(1)
Title
:
STRUCTURAL MECHANISM OF INHIBITION OF THE RHO TRANSCRIPTION TERMINATION FACTOR BY THE ANTIBIOTIC 5A-FORMYLBICYCLOMYCIN (FB)
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
:
3.15
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; 5A-Formylbicyclomycin; Fb; 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
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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: 5A-FORMYLBICYCLOMYCIN (FBa)
2b: 5A-FORMYLBICYCLOMYCIN (FBb)
2c: 5A-FORMYLBICYCLOMYCIN (FBc)
2d: 5A-FORMYLBICYCLOMYCIN (FBd)
2e: 5A-FORMYLBICYCLOMYCIN (FBe)
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
FB
-1
Ligand/Ion
5A-FORMYLBICYCLOMYCIN
3
MG
-1
Ligand/Ion
MAGNESIUM ION
[
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Sites
(3, 3)
Info
All Sites
1: AC6 (SOFTWARE)
2: BC3 (SOFTWARE)
3: BC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC6
SOFTWARE
THR F:185 , ARG F:212 , GLU F:215 , AGS F:6600 , FB F:6701
BINDING SITE FOR RESIDUE MG F 6601
2
BC3
SOFTWARE
ARG E:366 , GLU E:369 , THR F:158 , PRO F:180 , LYS F:181 , ALA F:182 , GLY F:183 , LYS F:184 , THR F:185 , MET F:186 , ARG F:212 , PHE F:355 , MG F:6601 , FB F:6701
BINDING SITE FOR RESIDUE AGS F 6600
3
BC8
SOFTWARE
LYS E:336 , GLY E:337 , ARG E:366 , LYS F:184 , ILE F:209 , ASP F:210 , GLU F:211 , ARG F:212 , ASP F:265 , SER F:266 , ARG F:269 , THR F:323 , AGS F:6600 , MG F:6601
BINDING SITE FOR RESIDUE FB F 6701
[
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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)
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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_d1xpra1 (A:1-47)
1b: SCOP_d1xprb1 (B:1-47)
1c: SCOP_d1xprc1 (C:1-47)
1d: SCOP_d1xprd1 (D:1-47)
1e: SCOP_d1xpre1 (E:1-47)
1f: SCOP_d1xprf1 (F:1-47)
2a: SCOP_d1xpra2 (A:48-126)
2b: SCOP_d1xprb2 (B:48-126)
2c: SCOP_d1xprc2 (C:48-126)
2d: SCOP_d1xprd2 (D:48-126)
2e: SCOP_d1xpre2 (E:48-126)
2f: SCOP_d1xprf2 (F:48-126)
3a: SCOP_d1xpra3 (A:129-417)
3b: SCOP_d1xprb3 (B:129-417)
3c: SCOP_d1xprc3 (C:129-417)
3d: SCOP_d1xprd3 (D:129-417)
3e: SCOP_d1xpre3 (E:129-417)
3f: SCOP_d1xprf3 (F:129-417)
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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
d1xpra1
A:1-47
1b
d1xprb1
B:1-47
1c
d1xprc1
C:1-47
1d
d1xprd1
D:1-47
1e
d1xpre1
E:1-47
1f
d1xprf1
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
d1xpra2
A:48-126
2b
d1xprb2
B:48-126
2c
d1xprc2
C:48-126
2d
d1xprd2
D:48-126
2e
d1xpre2
E:48-126
2f
d1xprf2
F: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
d1xpra3
A:129-417
3b
d1xprb3
B:129-417
3c
d1xprc3
C:129-417
3d
d1xprd3
D:129-417
3e
d1xpre3
E:129-417
3f
d1xprf3
F:129-417
[
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1xprE02 (E:129-417)
1b: CATH_1xprA02 (A:129-417)
1c: CATH_1xprB02 (B:129-417)
1d: CATH_1xprC02 (C:129-417)
1e: CATH_1xprD02 (D:129-417)
1f: CATH_1xprF02 (F:129-417)
2a: CATH_1xprA01 (A:1-126)
2b: CATH_1xprB01 (B:1-126)
2c: CATH_1xprC01 (C:1-126)
2d: CATH_1xprD01 (D:1-126)
2e: CATH_1xprE01 (E:1-126)
2f: CATH_1xprF01 (F:1-126)
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(
)
(
)
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
1xprE02
E:129-417
1b
1xprA02
A:129-417
1c
1xprB02
B:129-417
1d
1xprC02
C:129-417
1e
1xprD02
D:129-417
1f
1xprF02
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
1xprA01
A:1-126
2b
1xprB01
B:1-126
2c
1xprC01
C:1-126
2d
1xprD01
D:1-126
2e
1xprE01
E:1-126
2f
1xprF01
F:1-126
[
close CATH info
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Pfam Domains
(3, 18)
Info
all PFAM domains
1a: PFAM_Rho_N_1xprF01 (F:5-47)
1b: PFAM_Rho_N_1xprF02 (F:5-47)
1c: PFAM_Rho_N_1xprF03 (F:5-47)
1d: PFAM_Rho_N_1xprF04 (F:5-47)
1e: PFAM_Rho_N_1xprF05 (F:5-47)
1f: PFAM_Rho_N_1xprF06 (F:5-47)
2a: PFAM_Rho_RNA_bind_1xprF07 (F:49-126)
2b: PFAM_Rho_RNA_bind_1xprF08 (F:49-126)
2c: PFAM_Rho_RNA_bind_1xprF09 (F:49-126)
2d: PFAM_Rho_RNA_bind_1xprF10 (F:49-126)
2e: PFAM_Rho_RNA_bind_1xprF11 (F:49-126)
2f: PFAM_Rho_RNA_bind_1xprF12 (F:49-126)
3a: PFAM_ATP_synt_ab_1xprF13 (F:157-365)
3b: PFAM_ATP_synt_ab_1xprF14 (F:157-365)
3c: PFAM_ATP_synt_ab_1xprF15 (F:157-365)
3d: PFAM_ATP_synt_ab_1xprF16 (F:157-365)
3e: PFAM_ATP_synt_ab_1xprF17 (F:157-365)
3f: PFAM_ATP_synt_ab_1xprF18 (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-1xprF01
F:5-47
1b
Rho_N-1xprF02
F:5-47
1c
Rho_N-1xprF03
F:5-47
1d
Rho_N-1xprF04
F:5-47
1e
Rho_N-1xprF05
F:5-47
1f
Rho_N-1xprF06
F:5-47
Clan
:
OB
(224)
Family
:
Rho_RNA_bind
(5)
Escherichia coli (strain K12)
(5)
2a
Rho_RNA_bind-1xprF07
F:49-126
2b
Rho_RNA_bind-1xprF08
F:49-126
2c
Rho_RNA_bind-1xprF09
F:49-126
2d
Rho_RNA_bind-1xprF10
F:49-126
2e
Rho_RNA_bind-1xprF11
F:49-126
2f
Rho_RNA_bind-1xprF12
F:49-126
Clan
:
P-loop_NTPase
(1112)
Family
:
ATP-synt_ab
(44)
Escherichia coli (strain K12)
(5)
3a
ATP-synt_ab-1xprF13
F:157-365
3b
ATP-synt_ab-1xprF14
F:157-365
3c
ATP-synt_ab-1xprF15
F:157-365
3d
ATP-synt_ab-1xprF16
F:157-365
3e
ATP-synt_ab-1xprF17
F:157-365
3f
ATP-synt_ab-1xprF18
F:157-365
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Asym.Unit (405 KB)
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