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3U4M
Asym. Unit
Info
Asym.Unit (83 KB)
Biol.Unit 1 (77 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN TTHL1 IN COMPLEX WITH 80NT 23S RNA FROM THERMUS THERMOPHILUS
Authors
:
A. G. Gabdulkhakov, N. A. Nevskaya, S. V. Nikonov
Date
:
10 Oct 11 (Deposition) - 08 Aug 12 (Release) - 23 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Rossmann Fold, Ribosomal Protein, Rrna, Rrna Binding, Ribosome, Rna- Rna Binding Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Tishchenko, A. Gabdulkhakov, N. Nevskaya, A. Sarskikh, O. Kostareva, E. Nikonova, A. Sycheva, S. Moshkovskii, M. Garber, S. Nikonov
High-Resolution Crystal Structure Of The Isolated Ribosomal L1 Stalk.
Acta Crystallogr. , Sect. D V. 68 1051 2012
[
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Hetero Components
(5, 21)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
3a: MALONATE ION (MLIa)
3b: MALONATE ION (MLIb)
3c: MALONATE ION (MLIc)
3d: MALONATE ION (MLId)
3e: MALONATE ION (MLIe)
3f: MALONATE ION (MLIf)
3g: MALONATE ION (MLIg)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
4e: SODIUM ION (NAe)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
2
Ligand/Ion
CHLORIDE ION
2
MG
5
Ligand/Ion
MAGNESIUM ION
3
MLI
7
Ligand/Ion
MALONATE ION
4
NA
5
Ligand/Ion
SODIUM ION
5
SO4
2
Ligand/Ion
SULFATE ION
[
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Sites
(21, 21)
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)
21: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:197 , THR A:207 , PHE A:208 , LEU A:209
BINDING SITE FOR RESIDUE SO4 A 301
02
AC2
SOFTWARE
ALA A:33 , ALA A:35 , PHE A:37 , ASP A:38 , GLU A:39 , ILE A:83 , LYS A:84 , GLU A:87 , ALA A:178 , SER A:179 , MG A:305 , HOH A:417
BINDING SITE FOR RESIDUE MLI A 302
03
AC3
SOFTWARE
ALA A:112 , ILE A:156 , ARG A:160 , ILE A:161 , GLU A:162 , HOH A:453 , HOH A:457
BINDING SITE FOR RESIDUE MLI A 303
04
AC4
SOFTWARE
PHE A:37 , ASP A:38 , ALA A:78 , GLY A:80 , GLY A:96 , GLU A:97 , GLU A:98 , HOH A:474
BINDING SITE FOR RESIDUE MLI A 304
05
AC5
SOFTWARE
ALA A:33 , ALA A:35 , PHE A:37 , GLU A:39 , MLI A:302
BINDING SITE FOR RESIDUE MG A 305
06
AC6
SOFTWARE
GLU A:81
BINDING SITE FOR RESIDUE CL A 306
07
AC7
SOFTWARE
GLY A:60 , THR A:61 , HIS A:199
BINDING SITE FOR RESIDUE CL A 307
08
AC8
SOFTWARE
ARG A:6 , LEU A:10 , THR A:34 , HOH A:408 , HOH A:409
BINDING SITE FOR RESIDUE NA A 308
09
AC9
SOFTWARE
ARG A:6 , LEU A:10 , LEU A:32 , ALA A:33 , THR A:34 , GLU A:39 , MET A:218 , GLY A:219
BINDING SITE FOR RESIDUE NA A 309
10
BC1
SOFTWARE
ARG A:6 , HOH A:466 , C B:2129 , U B:2130
BINDING SITE FOR RESIDUE NA A 310
11
BC2
SOFTWARE
GLU A:42 , THR A:216 , THR A:217 , G B:2123 , C B:2175 , A B:2176
BINDING SITE FOR RESIDUE NA A 311
12
BC3
SOFTWARE
C B:2175 , A B:2176 , HOH B:2304 , HOH B:2321 , HOH B:2372 , HOH B:2375 , HOH B:2376 , HOH B:2383 , HOH B:2388
BINDING SITE FOR RESIDUE SO4 B 2201
13
BC4
SOFTWARE
A B:2134 , A B:2135 , G B:2156 , G B:2157
BINDING SITE FOR RESIDUE MLI B 2202
14
BC5
SOFTWARE
C B:2178 , C B:2179 , HOH B:2361 , HOH B:2362 , HOH B:2370 , HOH B:2391
BINDING SITE FOR RESIDUE MLI B 2203
15
BC6
SOFTWARE
U B:2130 , G B:2131 , C B:2139 , C B:2140 , G B:2152 , G B:2159 , HOH B:2371
BINDING SITE FOR RESIDUE MLI B 2204
16
BC7
SOFTWARE
A B:2119 , G B:2121 , A B:2170 , HOH B:2325 , HOH B:2334 , HOH B:2400 , HOH B:2410 , HOH B:2414 , HOH B:2416
BINDING SITE FOR RESIDUE MLI B 2205
17
BC8
SOFTWARE
U B:2122 , G B:2123 , HOH B:2302 , HOH B:2321 , HOH B:2325 , HOH B:2326
BINDING SITE FOR RESIDUE MG B 2206
18
BC9
SOFTWARE
HOH B:2304 , HOH B:2315 , HOH B:2321 , HOH B:2325 , HOH B:2363 , HOH B:2399
BINDING SITE FOR RESIDUE MG B 2207
19
CC1
SOFTWARE
G B:2120 , HOH B:2304 , HOH B:2376 , HOH B:2377 , HOH B:2378 , HOH B:2424
BINDING SITE FOR RESIDUE MG B 2208
20
CC2
SOFTWARE
U B:2172 , HOH B:2341 , HOH B:2379 , HOH B:2380 , HOH B:2381
BINDING SITE FOR RESIDUE MG B 2209
21
CC3
SOFTWARE
GLU A:42 , HIS A:44 , G B:2123 , G B:2124
BINDING SITE FOR RESIDUE NA B 2210
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: RIBOSOMAL_L1 (A:120-139)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIBOSOMAL_L1
PS01199
Ribosomal protein L1 signature.
RL1_THETH
121-140
1
A:120-139
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Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
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Asymmetric Unit 1
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Example Commands
Example Command
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select :A, :C
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)
ssbonds 100
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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Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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Asym.Unit (83 KB)
Header - Asym.Unit
Biol.Unit 1 (77 KB)
Header - Biol.Unit 1
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