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1Y39
Asym. Unit
Info
Asym.Unit (80 KB)
Biol.Unit 1 (38 KB)
Biol.Unit 2 (38 KB)
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(1)
Title
:
CO-EVOLUTION OF PROTEIN AND RNA STRUCTURES WITHIN A HIGHLY CONSERVED RIBOSOMAL DOMAIN
Authors
:
M. S. Dunstan, D. Guhathakurta, D. E. Draper, G. L. Conn
Date
:
24 Nov 04 (Deposition) - 22 Mar 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
X-Ray Crystal Structure, Choroplast-Like L11 Complex, Rrna, 23S Rna, Structural Protein-Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. S. Dunstan, D. Guhathakurta, D. E. Draper, G. L. Conn
Coevolution Of Protein And Rna Structures Within A Highly Conserved Ribosomal Domain
Chem. Biol. V. 12 201 2005
[
close entry info
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Hetero Components
(5, 26)
Info
All Hetero Components
1a: COBALT (III) ION (3COa)
1b: COBALT (III) ION (3COb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: GUANOSINE-5'-TRIPHOSPHATE (GTPa)
3b: GUANOSINE-5'-TRIPHOSPHATE (GTPb)
4a: POTASSIUM ION (Ka)
4b: POTASSIUM ION (Kb)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
5c: MAGNESIUM ION (MGc)
5d: MAGNESIUM ION (MGd)
5e: MAGNESIUM ION (MGe)
5f: MAGNESIUM ION (MGf)
5g: MAGNESIUM ION (MGg)
5h: MAGNESIUM ION (MGh)
5i: MAGNESIUM ION (MGi)
5j: MAGNESIUM ION (MGj)
5k: MAGNESIUM ION (MGk)
5l: MAGNESIUM ION (MGl)
5m: MAGNESIUM ION (MGm)
5n: MAGNESIUM ION (MGn)
5o: MAGNESIUM ION (MGo)
5p: MAGNESIUM ION (MGp)
5q: MAGNESIUM ION (MGq)
5r: MAGNESIUM ION (MGr)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3CO
2
Ligand/Ion
COBALT (III) ION
2
GOL
2
Ligand/Ion
GLYCEROL
3
GTP
2
Mod. Nucleotide
GUANOSINE-5'-TRIPHOSPHATE
4
K
2
Ligand/Ion
POTASSIUM ION
5
MG
18
Ligand/Ion
MAGNESIUM ION
[
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Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
G D:337
BINDING SITE FOR RESIDUE 3CO D 401
02
AC2
SOFTWARE
A D:319 , A D:320 , C D:322 , A D:323 , GOL D:704
BINDING SITE FOR RESIDUE K D 403
03
AC3
SOFTWARE
A C:119 , A C:120 , C C:122 , A C:123 , MG C:415
BINDING SITE FOR RESIDUE K C 404
04
AC4
SOFTWARE
A C:123 , G C:143 , U C:144
BINDING SITE FOR RESIDUE MG C 405
05
AC5
SOFTWARE
G D:313 , A D:320 , C D:322
BINDING SITE FOR RESIDUE MG D 406
06
AC6
SOFTWARE
U C:115 , U C:116 , A D:336
BINDING SITE FOR RESIDUE MG C 407
07
AC7
SOFTWARE
G C:113
BINDING SITE FOR RESIDUE MG C 408
08
AC8
SOFTWARE
A C:104 , G C:106 , HOH C:806
BINDING SITE FOR RESIDUE MG C 409
09
AC9
SOFTWARE
HOH D:811
BINDING SITE FOR RESIDUE MG D 410
10
BC1
SOFTWARE
A D:307 , A D:336 , G D:337 , HOH D:810
BINDING SITE FOR RESIDUE MG D 411
11
BC2
SOFTWARE
U D:308 , U D:310 , HOH D:809
BINDING SITE FOR RESIDUE MG D 412
12
BC3
SOFTWARE
G D:306
BINDING SITE FOR RESIDUE MG D 413
13
BC4
SOFTWARE
A C:120 , C C:122 , K C:404
BINDING SITE FOR RESIDUE MG C 415
14
BC5
SOFTWARE
G C:121
BINDING SITE FOR RESIDUE MG C 416
15
BC6
SOFTWARE
U D:308 , A D:311
BINDING SITE FOR RESIDUE MG D 418
16
BC7
SOFTWARE
U C:110
BINDING SITE FOR RESIDUE MG C 420
17
BC8
SOFTWARE
G C:106 , A C:107 , A C:136 , G C:137 , HOH C:807
BINDING SITE FOR RESIDUE MG C 421
18
BC9
SOFTWARE
G D:313 , A D:320
BINDING SITE FOR RESIDUE MG D 422
19
CC1
SOFTWARE
A D:319 , C D:322 , A D:323 , G D:343 , U D:344 , A D:346 , U D:347 , K D:403
BINDING SITE FOR RESIDUE GOL D 704
20
CC2
SOFTWARE
GTP C:101 , G C:157 , GTP D:301 , U D:358
BINDING SITE FOR RESIDUE GOL C 705
[
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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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: RIBOSOMAL_L11 (A:61-75,B:261-276)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIBOSOMAL_L11
PS00359
Ribosomal protein L11 signature.
RL11_GEOSE
118-133
2
A:61-75
B:261-276
[
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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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1y39a1 (A:2-75)
1b: SCOP_d1y39b1 (B:205-275)
View:
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Classes
(
)
(
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Folds
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(
)
Superfamilies
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(
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Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
Ribosomal protein L11, C-terminal domain
(96)
Family
:
Ribosomal protein L11, C-terminal domain
(96)
Protein domain
:
Ribosomal protein L11, C-terminal domain
(96)
Bacillus stearothermophilus [TaxId: 1422]
(8)
1a
d1y39a1
A:2-75
1b
d1y39b1
B:205-275
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1y39B00 (B:205-276)
1b: CATH_1y39A00 (A:2-75)
View:
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Classes
(
)
(
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Architectures
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
[code=1.10.10.250, no name defined]
(69)
[unclassified]
(3)
1a
1y39B00
B:205-276
1b
1y39A00
A:2-75
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Ribosomal_L11_1y39B01 (B:206-274)
1b: PFAM_Ribosomal_L11_1y39B02 (B:206-274)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Ribosomal_L11]
(35)
Family
:
Ribosomal_L11
(35)
Geobacillus stearothermophilus (Bacillus stearothermophilus)
(2)
1a
Ribosomal_L11-1y39B01
B:206-274
1b
Ribosomal_L11-1y39B02
B:206-274
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Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (80 KB)
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