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3R1L
Asym. Unit
Info
Asym.Unit (160 KB)
Biol.Unit 1 (77 KB)
Biol.Unit 2 (77 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CLASS I LIGASE RIBOZYME-SUBSTRATE PRELIGATION COMPLEX, C47U MUTANT, MG2+ BOUND
Authors
:
D. M. Shechner, D. P. Bartel
Date
:
10 Mar 11 (Deposition) - 31 Aug 11 (Release) - 21 Sep 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.12
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Ligase Ribozyme, Catalytic Rna, Ribozyme, Rna Binding Protein-Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. M. Shechner, D. P. Bartel
The Structural Basis Of Rna-Catalyzed Rna Polymerization.
Nat. Struct. Mol. Biol. V. 18 1036 2011
[
close entry info
]
Hetero Components
(3, 50)
Info
All Hetero Components
1a: ADENOSINE-5'-PHOSPHATE-2',3'-CYCLI... (A23a)
1b: ADENOSINE-5'-PHOSPHATE-2',3'-CYCLI... (A23b)
2a: GUANOSINE-5'-TRIPHOSPHATE (GTPa)
2b: GUANOSINE-5'-TRIPHOSPHATE (GTPb)
3a: MAGNESIUM ION (MGa)
3aa: MAGNESIUM ION (MGaa)
3ab: MAGNESIUM ION (MGab)
3ac: MAGNESIUM ION (MGac)
3ad: MAGNESIUM ION (MGad)
3ae: MAGNESIUM ION (MGae)
3af: MAGNESIUM ION (MGaf)
3ag: MAGNESIUM ION (MGag)
3ah: MAGNESIUM ION (MGah)
3ai: MAGNESIUM ION (MGai)
3aj: MAGNESIUM ION (MGaj)
3ak: MAGNESIUM ION (MGak)
3al: MAGNESIUM ION (MGal)
3am: MAGNESIUM ION (MGam)
3an: MAGNESIUM ION (MGan)
3ao: MAGNESIUM ION (MGao)
3ap: MAGNESIUM ION (MGap)
3aq: MAGNESIUM ION (MGaq)
3ar: MAGNESIUM ION (MGar)
3as: MAGNESIUM ION (MGas)
3at: MAGNESIUM ION (MGat)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
3j: MAGNESIUM ION (MGj)
3k: MAGNESIUM ION (MGk)
3l: MAGNESIUM ION (MGl)
3m: MAGNESIUM ION (MGm)
3n: MAGNESIUM ION (MGn)
3o: MAGNESIUM ION (MGo)
3p: MAGNESIUM ION (MGp)
3q: MAGNESIUM ION (MGq)
3r: MAGNESIUM ION (MGr)
3s: MAGNESIUM ION (MGs)
3t: MAGNESIUM ION (MGt)
3u: MAGNESIUM ION (MGu)
3v: MAGNESIUM ION (MGv)
3w: MAGNESIUM ION (MGw)
3x: MAGNESIUM ION (MGx)
3y: MAGNESIUM ION (MGy)
3z: MAGNESIUM ION (MGz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
A23
2
Mod. Nucleotide
ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2
GTP
2
Mod. Nucleotide
GUANOSINE-5'-TRIPHOSPHATE
3
MG
46
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(36, 36)
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)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
A C:31 , A C:32 , HOH C:1044 , HOH C:1045 , HOH C:1046 , HOH C:1047
BINDING SITE FOR RESIDUE MG C 1019
02
AC2
SOFTWARE
GTP C:1 , G C:2 , HOH C:1048 , HOH C:1049 , HOH C:1050 , HOH C:1051
BINDING SITE FOR RESIDUE MG C 1020
03
AC3
SOFTWARE
C C:70 , G C:72 , U C:106 , HOH C:1052 , HOH C:1053 , HOH C:1054 , HOH C:1071
BINDING SITE FOR RESIDUE MG C 1021
04
AC4
SOFTWARE
A C:95 , A C:96 , HOH C:1072
BINDING SITE FOR RESIDUE MG C 1023
05
AC5
SOFTWARE
A C:97
BINDING SITE FOR RESIDUE MG C 1024
06
AC6
SOFTWARE
HOH C:1055 , HOH C:1056 , HOH C:1057 , HOH C:1058 , HOH C:1059 , HOH C:1060
BINDING SITE FOR RESIDUE MG C 1027
07
AC7
SOFTWARE
U C:68
BINDING SITE FOR RESIDUE MG C 1028
08
AC8
SOFTWARE
U C:47
BINDING SITE FOR RESIDUE MG C 1029
09
AC9
SOFTWARE
G C:45 , G F:45
BINDING SITE FOR RESIDUE MG C 1030
10
BC1
SOFTWARE
A C:4 , A C:114 , A C:115 , HOH C:1061 , HOH C:1062
BINDING SITE FOR RESIDUE MG C 1031
11
BC2
SOFTWARE
A C:1005
BINDING SITE FOR RESIDUE MG C 1032
12
BC3
SOFTWARE
C C:70 , HOH C:1063 , HOH C:1064 , HOH C:1065 , HOH C:1066 , HOH C:1067 , HOH C:1068
BINDING SITE FOR RESIDUE MG C 1033
13
BC4
SOFTWARE
GTP C:1 , C C:7 , HOH C:1069
BINDING SITE FOR RESIDUE MG C 1034
14
BC5
SOFTWARE
GTP C:1 , G C:2 , U C:8
BINDING SITE FOR RESIDUE MG C 1035
15
BC6
SOFTWARE
C C:40 , G C:41 , G C:44
BINDING SITE FOR RESIDUE MG C 1036
16
BC7
SOFTWARE
A C:43
BINDING SITE FOR RESIDUE MG C 1037
17
BC8
SOFTWARE
C C:1009
BINDING SITE FOR RESIDUE MG C 1039
18
BC9
SOFTWARE
G C:92 , U C:93
BINDING SITE FOR RESIDUE MG C 1040
19
CC1
SOFTWARE
A B:-1 , GTP C:1 , A C:29 , C C:30
BINDING SITE FOR RESIDUE MG C 1041
20
CC2
SOFTWARE
C C:30 , A C:31 , HOH C:1069 , HOH C:1073
BINDING SITE FOR RESIDUE MG C 1042
21
CC3
SOFTWARE
A F:31 , A F:32 , HOH F:1040 , HOH F:1041 , HOH F:1042 , HOH F:1043
BINDING SITE FOR RESIDUE MG F 1019
22
CC4
SOFTWARE
GTP F:1 , G F:2 , HOH F:1044 , HOH F:1045 , HOH F:1046 , HOH F:1047
BINDING SITE FOR RESIDUE MG F 1020
23
CC5
SOFTWARE
C F:70 , A F:71 , G F:72 , U F:106 , HOH F:1048 , HOH F:1049 , HOH F:1050
BINDING SITE FOR RESIDUE MG F 1021
24
CC6
SOFTWARE
G F:45
BINDING SITE FOR RESIDUE MG F 1024
25
CC7
SOFTWARE
U F:68
BINDING SITE FOR RESIDUE MG F 1026
26
CC8
SOFTWARE
U F:47
BINDING SITE FOR RESIDUE MG F 1027
27
CC9
SOFTWARE
A F:4 , A F:6
BINDING SITE FOR RESIDUE MG F 1028
28
DC1
SOFTWARE
A F:3 , A F:4
BINDING SITE FOR RESIDUE MG F 1029
29
DC2
SOFTWARE
A F:26 , G F:28 , A F:1005
BINDING SITE FOR RESIDUE MG F 1030
30
DC3
SOFTWARE
HOH F:1052 , HOH F:1053 , HOH F:1054 , HOH F:1055 , HOH F:1056 , HOH F:1057
BINDING SITE FOR RESIDUE MG F 1031
31
DC4
SOFTWARE
U F:34 , C F:35 , G F:75 , U F:76
BINDING SITE FOR RESIDUE MG F 1032
32
DC5
SOFTWARE
GTP F:1 , C F:7 , HOH F:1058
BINDING SITE FOR RESIDUE MG F 1033
33
DC6
SOFTWARE
GTP F:1 , U F:8
BINDING SITE FOR RESIDUE MG F 1034
34
DC7
SOFTWARE
G F:41 , A F:42 , A F:43
BINDING SITE FOR RESIDUE MG F 1036
35
DC8
SOFTWARE
A F:43
BINDING SITE FOR RESIDUE MG F 1037
36
DC9
SOFTWARE
A E:-1 , GTP F:1 , A F:29 , C F:30 , U F:47
BINDING SITE FOR RESIDUE MG F 1038
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: RRM (A:10-89,D:10-89|-)
;
View:
Select:
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
A:10-89
D:10-89
-
[
close PROSITE info
]
Exons
(3, 6)
Info
All Exons
Exon 1.1 (A:7-25 | D:6-25)
Exon 1.2 (A:25-82 | D:25-82)
Exon 1.3 (A:83-98 | D:83-98)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000243563
1
ENSE00001052136
chr19:
41256779-41257386
608
SNRPA_HUMAN
1-25
25
2
A:7-25
D:6-25
19
20
1.2
ENST00000243563
2
ENSE00000707951
chr19:
41263237-41263409
173
SNRPA_HUMAN
25-82
58
2
A:25-82
D:25-82
58
58
1.3
ENST00000243563
3
ENSE00000707956
chr19:
41265336-41265515
180
SNRPA_HUMAN
83-142
60
2
A:83-98
D:83-98
16
16
1.4
ENST00000243563
4
ENSE00000707961
chr19:
41268806-41268979
174
SNRPA_HUMAN
143-200
58
0
-
-
1.5
ENST00000243563
5
ENSE00000842333
chr19:
41269492-41269580
89
SNRPA_HUMAN
201-230
30
0
-
-
1.6
ENST00000243563
6
ENSE00000842334
chr19:
41270913-41271290
378
SNRPA_HUMAN
230-282
53
0
-
-
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
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set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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show bonds with a radius of 100 units (=0.4Å)
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