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3IVK
Asym. Unit
Info
Asym.Unit (255 KB)
Biol.Unit 1 (125 KB)
Biol.Unit 2 (125 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC CORE OF AN RNA POLYMERASE RIBOZYME COMPLEXED WITH AN ANTIGEN BINDING ANTIBODY FRAGMENT
Authors
:
Y. Koldobskaya, E. M. Duguid, D. M. Shechner, S. Koide, A. A. Kossiakoff D. P. Bartel, J. A. Piccirilli
Date
:
01 Sep 09 (Deposition) - 02 Mar 10 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,H,L,M
Biol. Unit 1: H,L,M (1x)
Biol. Unit 2: A,B,C (1x)
Keywords
:
Catalytic Rna, Protein Rna Complex, Rna Polymerase Ribozyme, Rna Hairpin Epitope, Immune System - Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. M. Shechner, R. A. Grant, S. C. Bagby, Y. Koldobskaya, J. A. Piccirilli, D. P. Bartel
Crystal Structure Of The Catalytic Core Of An Rna-Polymeras Ribozyme.
Science V. 326 1271 2009
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 37)
Info
All Hetero Components
1a: CADMIUM ION (CDa)
1b: CADMIUM ION (CDb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
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)
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
CD
2
Ligand/Ion
CADMIUM ION
2
CL
2
Ligand/Ion
CHLORIDE ION
3
MG
33
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(37, 37)
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)
37: EC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:65 , ASP B:2 , A M:21
BINDING SITE FOR RESIDUE CD B 214
02
AC2
SOFTWARE
A C:21 , ASP H:65 , ASP L:2
BINDING SITE FOR RESIDUE CD L 214
03
AC3
SOFTWARE
ASP B:186 , ASP L:186
BINDING SITE FOR RESIDUE MG L 215
04
AC4
SOFTWARE
ARG A:110 , SER B:51
BINDING SITE FOR RESIDUE CL B 215
05
AC5
SOFTWARE
ARG H:110 , SER L:51
BINDING SITE FOR RESIDUE CL L 216
06
AC6
SOFTWARE
HOH M:138 , HOH M:139 , HOH M:140 , HOH M:141 , HOH M:142 , HOH M:143
BINDING SITE FOR RESIDUE MG M 122
07
AC7
SOFTWARE
HOH M:144 , HOH M:145 , HOH M:146 , HOH M:147 , HOH M:148 , HOH M:149
BINDING SITE FOR RESIDUE MG M 123
08
AC8
SOFTWARE
HOH M:150 , HOH M:151 , HOH M:152 , HOH M:153 , HOH M:154 , HOH M:155
BINDING SITE FOR RESIDUE MG M 124
09
AC9
SOFTWARE
HOH M:156 , HOH M:157 , HOH M:158 , HOH M:159 , HOH M:160 , HOH M:161
BINDING SITE FOR RESIDUE MG M 125
10
BC1
SOFTWARE
HOH H:227 , HOH H:228 , HOH M:162 , HOH M:163 , HOH M:164
BINDING SITE FOR RESIDUE MG M 126
11
BC2
SOFTWARE
A M:31 , A M:32
BINDING SITE FOR RESIDUE MG M 127
12
BC3
SOFTWARE
G M:2 , HOH M:165 , HOH M:166 , HOH M:167 , HOH M:168 , HOH M:169
BINDING SITE FOR RESIDUE MG M 128
13
BC4
SOFTWARE
HOH M:170 , HOH M:171 , HOH M:172 , HOH M:173 , HOH M:174 , HOH M:175
BINDING SITE FOR RESIDUE MG M 129
14
BC5
SOFTWARE
A M:71 , G M:72 , U M:106
BINDING SITE FOR RESIDUE MG M 130
15
BC6
SOFTWARE
G M:45 , G M:46 , C M:47
BINDING SITE FOR RESIDUE MG M 131
16
BC7
SOFTWARE
HOH M:176 , HOH M:177 , HOH M:178 , HOH M:179 , HOH M:180 , HOH M:181
BINDING SITE FOR RESIDUE MG M 132
17
BC8
SOFTWARE
G M:77
BINDING SITE FOR RESIDUE MG M 133
18
BC9
SOFTWARE
HOH M:182 , HOH M:183 , HOH M:184 , HOH M:185 , HOH M:186 , HOH M:187
BINDING SITE FOR RESIDUE MG M 134
19
CC1
SOFTWARE
G M:41
BINDING SITE FOR RESIDUE MG M 135
20
CC2
SOFTWARE
A M:56 , C M:63
BINDING SITE FOR RESIDUE MG M 136
21
CC3
SOFTWARE
G M:74
BINDING SITE FOR RESIDUE MG M 137
22
CC4
SOFTWARE
HOH C:138 , HOH C:139 , HOH C:140 , HOH C:141 , HOH C:142 , HOH C:143
BINDING SITE FOR RESIDUE MG C 122
23
CC5
SOFTWARE
HOH C:144 , HOH C:145 , HOH C:146 , HOH C:147 , HOH C:148 , HOH C:149
BINDING SITE FOR RESIDUE MG C 123
24
CC6
SOFTWARE
HOH C:150 , HOH C:151 , HOH C:152 , HOH C:153 , HOH C:154 , HOH C:155
BINDING SITE FOR RESIDUE MG C 124
25
CC7
SOFTWARE
HOH C:156 , HOH C:157 , HOH C:158 , HOH C:159 , HOH C:160 , HOH C:161
BINDING SITE FOR RESIDUE MG C 125
26
CC8
SOFTWARE
HOH A:227 , HOH C:162 , HOH C:163 , HOH C:164 , HOH C:165
BINDING SITE FOR RESIDUE MG C 126
27
CC9
SOFTWARE
A C:31 , A C:32
BINDING SITE FOR RESIDUE MG C 127
28
DC1
SOFTWARE
G C:2 , HOH C:166 , HOH C:167 , HOH C:168 , HOH C:169 , HOH C:170
BINDING SITE FOR RESIDUE MG C 128
29
DC2
SOFTWARE
HOH C:171 , HOH C:172 , HOH C:173 , HOH C:174 , HOH C:175 , HOH C:176
BINDING SITE FOR RESIDUE MG C 129
30
DC3
SOFTWARE
A C:71 , G C:72 , U C:106
BINDING SITE FOR RESIDUE MG C 130
31
DC4
SOFTWARE
G C:45 , G C:46 , C C:47
BINDING SITE FOR RESIDUE MG C 131
32
DC5
SOFTWARE
HOH C:177 , HOH C:178 , HOH C:179 , HOH C:180 , HOH C:181 , HOH C:182
BINDING SITE FOR RESIDUE MG C 132
33
DC6
SOFTWARE
G C:77
BINDING SITE FOR RESIDUE MG C 133
34
DC7
SOFTWARE
HOH C:183 , HOH C:184 , HOH C:185 , HOH C:186 , HOH C:187 , HOH C:188
BINDING SITE FOR RESIDUE MG C 134
35
DC8
SOFTWARE
G C:41
BINDING SITE FOR RESIDUE MG C 135
36
DC9
SOFTWARE
A C:56 , C C:63
BINDING SITE FOR RESIDUE MG C 136
37
EC1
SOFTWARE
G C:74
BINDING SITE FOR RESIDUE MG C 137
[
close Site info
]
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3ivkb1 (B:1-108)
1b: SCOP_d3ivkl1 (L:1-108)
2a: SCOP_d3ivkb2 (B:109-213)
2b: SCOP_d3ivkl2 (L:109-213)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Mouse (Mus musculus) [TaxId: 10090]
(360)
1a
d3ivkb1
B:1-108
1b
d3ivkl1
L:1-108
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Mouse (Mus musculus) [TaxId: 10090]
(309)
2a
d3ivkb2
B:109-213
2b
d3ivkl2
L:109-213
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_3ivkB02 (B:110-213)
1b: CATH_3ivkL02 (L:110-213)
1c: CATH_3ivkA02 (A:126-225)
1d: CATH_3ivkH02 (H:126-225)
1e: CATH_3ivkA01 (A:3-125)
1f: CATH_3ivkH01 (H:3-125)
View:
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Classes
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(
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Architectures
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Mus musculus. Organism_taxid: 10090.
(7)
1a
3ivkB02
B:110-213
1b
3ivkL02
L:110-213
1c
3ivkA02
A:126-225
1d
3ivkH02
H:126-225
1e
3ivkA01
A:3-125
1f
3ivkH01
H:3-125
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
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 H
Chain L
Chain M
Asymmetric Unit 1
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Asym.Unit (255 KB)
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