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4BLW
Biol. Unit 1
Info
Asym.Unit (110 KB)
Biol.Unit 1 (55 KB)
Biol.Unit 2 (53 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ESCHERICHIA COLI 23S RRNA (A2030-N6)-METHYLTRANSFERASE RLMJ IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE (ADOHCY) AND ADENOSINE MONOPHOSPHATE ( AMP)
Authors
:
A. S. Punekar, J. Liljeruhm, T. R. Shepherd, A. C. Forster, M. Selmer
Date
:
04 May 13 (Deposition) - 21 Aug 13 (Release) - 17 Dec 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Transferase, N6-Methyladenine, Rossmann-Like Fold, Subdomain Insertion
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. S. Punekar, J. Liljeruhm, T. R. Shepherd, A. C. Forster, M. Selmer
Structural And Functional Insights Into The Molecular Mechanism Of Rrna M6A Methyltransferase Rlmj.
Nucleic Acids Res. V. 41 9537 2013
[
close entry info
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Hetero Components
(5, 14)
Info
All Hetero Components
1a: ADENOSINE MONOPHOSPHATE (AMPa)
1b: ADENOSINE MONOPHOSPHATE (AMPb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: S-ADENOSYL-L-HOMOCYSTEINE (SAHa)
5b: S-ADENOSYL-L-HOMOCYSTEINE (SAHb)
6a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AMP
1
Ligand/Ion
ADENOSINE MONOPHOSPHATE
2
EDO
9
Ligand/Ion
1,2-ETHANEDIOL
3
GOL
2
Ligand/Ion
GLYCEROL
4
NA
-1
Ligand/Ion
SODIUM ION
5
SAH
1
Ligand/Ion
S-ADENOSYL-L-HOMOCYSTEINE
6
SO4
1
Ligand/Ion
SULFATE ION
[
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Sites
(17, 17)
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: CC3 (SOFTWARE)
16: CC4 (SOFTWARE)
17: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:4 , HIS A:9 , ASN A:12 , GLU A:60 , VAL A:199 , MET A:235 , NA A:1294 , HOH A:2015 , HOH A:2128 , HOH A:2201 , HOH A:2202
BINDING SITE FOR RESIDUE AMP A1281
02
AC2
SOFTWARE
LEU A:2 , TYR A:4 , LYS A:18 , HIS A:19 , THR A:41 , HIS A:42 , ALA A:43 , GLY A:44 , GLY A:99 , SER A:100 , GLU A:118 , LEU A:119 , HIS A:120 , ALA A:142 , ASP A:143 , GLY A:144 , ASP A:164 , HOH A:2003 , HOH A:2006 , HOH A:2009 , HOH A:2041 , HOH A:2042
BINDING SITE FOR RESIDUE SAH A1282
03
AC3
SOFTWARE
ALA A:66 , ARG A:67 , LYS A:185 , ARG A:186 , PHE A:187 , ALA A:188 , EDO A:1285 , HOH A:2060 , HOH A:2061 , HOH A:2146 , HOH A:2149 , HOH A:2150 , HOH A:2204
BINDING SITE FOR RESIDUE GOL A1283
04
AC4
SOFTWARE
VAL A:155 , SER A:156 , ARG A:157 , HOH A:2205 , GLU B:110 , GLN B:111
BINDING SITE FOR RESIDUE GOL A1284
05
AC5
SOFTWARE
ARG A:67 , PRO A:266 , GOL A:1283 , HOH A:2147 , HOH A:2192
BINDING SITE FOR RESIDUE EDO A1285
06
AC6
SOFTWARE
HIS A:13 , GLU A:60 , GLU A:63 , HOH A:2016 , HOH A:2055 , HOH A:2056
BINDING SITE FOR RESIDUE EDO A1286
07
AC7
SOFTWARE
LEU A:106 , ARG B:90
BINDING SITE FOR RESIDUE EDO A1287
08
AC8
SOFTWARE
SER A:7 , PHE A:8 , HIS A:9 , ALA A:10 , LEU A:50 , ALA A:55 , THR A:58 , GLY A:59 , GLU A:60 , TYR A:61
BINDING SITE FOR RESIDUE EDO A1288
09
AC9
SOFTWARE
PRO A:228 , THR A:269 , GLY A:270
BINDING SITE FOR RESIDUE EDO A1289
10
BC1
SOFTWARE
PRO A:266 , ALA A:267
BINDING SITE FOR RESIDUE EDO A1290
11
BC2
SOFTWARE
LYS A:30 , LEU A:106 , LEU A:107 , LEU A:108 , HOH A:2206 , HOH A:2207
BINDING SITE FOR RESIDUE EDO A1291
12
BC3
SOFTWARE
LEU A:39 , GLN A:115 , LEU A:116 , THR A:117 , ARG A:138 , GLU A:140 , GLN A:147 , LYS A:151 , HOH A:2039
BINDING SITE FOR RESIDUE EDO A1292
13
BC4
SOFTWARE
ARG A:47 , GLU A:130 , SO4 A:1295 , HOH A:2107
BINDING SITE FOR RESIDUE EDO A1293
14
BC5
SOFTWARE
TYR A:4 , PRO A:165 , PRO A:166 , TRP A:195 , AMP A:1281 , HOH A:2019 , HOH A:2126 , HOH A:2128
BINDING SITE FOR RESIDUE NA A1294
15
CC3
SOFTWARE
ARG A:105 , LYS A:133 , HOH A:2109 , HIS B:87 , PHE B:88 , ASN B:89 , ARG B:90 , SER B:91 , HOH B:2055
BINDING SITE FOR RESIDUE EDO B1285
16
CC4
SOFTWARE
GLU A:110 , HOH A:2096 , TRP B:69 , LYS B:86 , ASN B:89 , ARG B:90
BINDING SITE FOR RESIDUE EDO B1288
17
CC6
SOFTWARE
HIS A:87 , EDO A:1293 , HOH A:2047 , HOH A:2094 , HOH A:2208 , HIS B:87
BINDING SITE FOR RESIDUE SO4 A1295
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: N6_MTASE (A:161-167,A:241-247)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
N6_MTASE
PS00092
N-6 Adenine-specific DNA methylases signature.
RLMJ_ECOLI
161-167
241-247
2
A:161-167
-
A:241-247
-
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d4blwa_ (A:)
1b: SCOP_d4blwb_ (B:)
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Classes
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(
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Families
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
S-adenosyl-L-methionine-dependent methyltransferases
(533)
Superfamily
:
S-adenosyl-L-methionine-dependent methyltransferases
(533)
Family
:
automated matches
(94)
Protein domain
:
automated matches
(94)
Escherichia coli K-12 [TaxId: 83333]
(5)
1a
d4blwa_
A:
1b
d4blwb_
B:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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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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Atom Selection
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Protein
Nucleic
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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select chains 'A' and 'C'
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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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Asym.Unit (110 KB)
Header - Asym.Unit
Biol.Unit 1 (55 KB)
Header - Biol.Unit 1
Biol.Unit 2 (53 KB)
Header - Biol.Unit 2
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