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3K0J
Biol. Unit 2
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Asym.Unit (136 KB)
Biol.Unit 1 (68 KB)
Biol.Unit 2 (66 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE E. COLI THIM RIBOSWITCH IN COMPLEX WITH THIAMINE PYROPHOSPHATE AND THE U1A CRYSTALLIZATION MODULE
Authors
:
N. Kulshina, T. E. Edwards, A. R. Ferre-D'Amare
Date
:
24 Sep 09 (Deposition) - 22 Dec 09 (Release) - 12 Jan 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,C,E (1x)
Biol. Unit 2: B,D,F (1x)
Keywords
:
Riboswitch, Rna, Thi-Box, Thim, U1A Protein, Acetylation, Mrna Processing, Mrna Splicing, Nucleus, Phosphoprotein, Ribonucleoprotein, Rna-Binding, Spliceosome, Rna/Rna Binding Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Kulshina, T. E. Edwards, A. R. Ferre-D'Amare
Thermodynamic Analysis Of Ligand Binding And Ligand Binding-Induced Tertiary Structure Formation By The Thiamine Pyrophosphate Riboswitch.
Rna V. 16 186 2010
(for further references see the
PDB file header
)
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
1g: MAGNESIUM ION (MGg)
1h: MAGNESIUM ION (MGh)
2a: THIAMINE DIPHOSPHATE (TPPa)
2b: THIAMINE DIPHOSPHATE (TPPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
TPP
1
Ligand/Ion
THIAMINE DIPHOSPHATE
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Sites
(3, 3)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC5 (SOFTWARE)
3: BC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
G F:114 , G F:140 , G F:142 , A F:143 , C F:157 , C F:158 , G F:172 , A F:175 , G F:176 , C F:177 , MG F:703 , MG F:708
BINDING SITE FOR RESIDUE TPP F 602
2
AC5
SOFTWARE
U F:159 , G F:160 , G F:178 , TPP F:602 , MG F:708
BINDING SITE FOR RESIDUE MG F 703
3
BC1
SOFTWARE
G F:178 , TPP F:602 , MG F:703
BINDING SITE FOR RESIDUE MG F 708
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: RRM (B:310-389,D:510-589|-)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RRM
PS50102
Eukaryotic RNA Recognition Motif (RRM) profile.
SNRPA_HUMAN
10-89
208-282
2
-
B:310-389
-
D:510-589
-
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3k0ja_ (A:)
1b: SCOP_d3k0jb_ (B:)
1c: SCOP_d3k0jc_ (C:)
1d: SCOP_d3k0jd_ (D:)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
RNA-binding domain, RBD
(289)
Family
:
Canonical RBD
(214)
Protein domain
:
automated matches
(24)
Human (Homo sapiens) [TaxId: 9606]
(21)
1a
d3k0ja_
A:
1b
d3k0jb_
B:
1c
d3k0jc_
C:
1d
d3k0jd_
D:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3k0jC00 (C:404-489)
1b: CATH_3k0jA00 (A:206-297)
1c: CATH_3k0jB00 (B:306-397)
1d: CATH_3k0jD00 (D:506-589)
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(
)
(
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.330, no name defined]
(307)
Human (Homo sapiens)
(81)
1a
3k0jC00
C:404-489
1b
3k0jA00
A:206-297
1c
3k0jB00
B:306-397
1d
3k0jD00
D:506-589
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_RRM_1_3k0jD01 (D:512-583)
1b: PFAM_RRM_1_3k0jD02 (D:512-583)
1c: PFAM_RRM_1_3k0jD03 (D:512-583)
1d: PFAM_RRM_1_3k0jD04 (D:512-583)
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Clans
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Clan
:
RRM
(206)
Family
:
RRM_1
(131)
Homo sapiens (Human)
(94)
1a
RRM_1-3k0jD01
D:512-583
1b
RRM_1-3k0jD02
D:512-583
1c
RRM_1-3k0jD03
D:512-583
1d
RRM_1-3k0jD04
D:512-583
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Asymmetric Unit 1
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Asym.Unit (136 KB)
Header - Asym.Unit
Biol.Unit 1 (68 KB)
Header - Biol.Unit 1
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Header - Biol.Unit 2
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