PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4BLV
Asym. Unit
Info
Asym.Unit (114 KB)
Biol.Unit 1 (56 KB)
Biol.Unit 2 (55 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF ESCHERICHIA COLI 23S RRNA (A2030-N6)-METHYLTRANSFERASE RLMJ IN COMPLEX WITH S-ADENOSYLMETHIONINE (ADOMET)
Authors
:
A. S. Punekar, J. Liljeruhm, T. R. Shepherd, A. C. Forster, M. Selmer
Date
:
04 May 13 (Deposition) - 21 Aug 13 (Release) - 13 Nov 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
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
]
Hetero Components
(5, 34)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1aa: 1,2-ETHANEDIOL (EDOaa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
1m: 1,2-ETHANEDIOL (EDOm)
1n: 1,2-ETHANEDIOL (EDOn)
1o: 1,2-ETHANEDIOL (EDOo)
1p: 1,2-ETHANEDIOL (EDOp)
1q: 1,2-ETHANEDIOL (EDOq)
1r: 1,2-ETHANEDIOL (EDOr)
1s: 1,2-ETHANEDIOL (EDOs)
1t: 1,2-ETHANEDIOL (EDOt)
1u: 1,2-ETHANEDIOL (EDOu)
1v: 1,2-ETHANEDIOL (EDOv)
1w: 1,2-ETHANEDIOL (EDOw)
1x: 1,2-ETHANEDIOL (EDOx)
1y: 1,2-ETHANEDIOL (EDOy)
1z: 1,2-ETHANEDIOL (EDOz)
2a: GLYCEROL (GOLa)
3a: DI(HYDROXYETHYL)ETHER (PEGa)
3b: DI(HYDROXYETHYL)ETHER (PEGb)
4a: S-ADENOSYLMETHIONINE (SAMa)
4b: S-ADENOSYLMETHIONINE (SAMb)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
27
Ligand/Ion
1,2-ETHANEDIOL
2
GOL
1
Ligand/Ion
GLYCEROL
3
PEG
2
Ligand/Ion
DI(HYDROXYETHYL)ETHER
4
SAM
2
Ligand/Ion
S-ADENOSYLMETHIONINE
5
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(34, 34)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:2 , TYR A:4 , HIS A:6 , 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:2002 , HOH A:2007 , HOH A:2058 , HOH A:2059
BINDING SITE FOR RESIDUE SAM A1281
02
AC2
SOFTWARE
LYS A:30 , LEU A:106 , LEU A:107 , LEU A:108 , ARG A:109 , HOH A:2120 , HOH A:2239 , HOH A:2240 , ARG B:90
BINDING SITE FOR RESIDUE GOL A1282
03
AC3
SOFTWARE
VAL A:199 , LEU A:200 , ARG A:201 , ASP A:229 , SER A:230 , HOH A:2192 , HOH A:2195
BINDING SITE FOR RESIDUE PEG A1283
04
AC4
SOFTWARE
HIS A:13 , MET A:235 , EDO A:1285 , HOH A:2066 , HOH A:2067
BINDING SITE FOR RESIDUE EDO A1284
05
AC5
SOFTWARE
HIS A:13 , GLU A:63 , EDO A:1284 , HOH A:2020 , HOH A:2071 , HOH A:2072
BINDING SITE FOR RESIDUE EDO A1285
06
AC6
SOFTWARE
VAL A:226 , LEU A:227 , VAL A:265 , ALA A:267 , THR A:269 , HOH A:2231
BINDING SITE FOR RESIDUE EDO A1286
07
AC7
SOFTWARE
HIS A:6 , HIS A:9 , ASN A:12 , ALA A:14 , ASP A:15 , MET A:235 , HOH A:2004 , HOH A:2023
BINDING SITE FOR RESIDUE EDO A1287
08
AC8
SOFTWARE
ARG A:201 , GLU A:223 , HIS A:271 , THR A:273
BINDING SITE FOR RESIDUE EDO A1288
09
AC9
SOFTWARE
PRO A:228 , ASP A:229 , GLY A:270 , HIS A:271
BINDING SITE FOR RESIDUE EDO A1289
10
BC1
SOFTWARE
ARG A:128 , PHE A:131 , GLN A:132 , VAL A:139 , HOH A:2139 , HOH A:2141
BINDING SITE FOR RESIDUE EDO A1290
11
BC2
SOFTWARE
THR A:189 , ILE A:191 , ASN A:244 , PRO A:245 , SO4 A:1297 , HOH A:2241
BINDING SITE FOR RESIDUE EDO A1291
12
BC3
SOFTWARE
PHE A:145 , ALA A:175 , HOH A:2150 , HOH A:2178
BINDING SITE FOR RESIDUE EDO A1292
13
BC4
SOFTWARE
SER A:3 , TYR A:4 , GLU A:168 , HOH A:2167
BINDING SITE FOR RESIDUE EDO A1293
14
BC5
SOFTWARE
SER A:7 , ALA A:45 , ARG A:47 , TYR A:48 , GLN A:49 , LEU A:126 , HOH A:2135
BINDING SITE FOR RESIDUE EDO A1294
15
BC6
SOFTWARE
PRO A:246 , TRP A:247 , LEU A:249 , GLU A:250 , TRP A:276 , HOH A:2218 , HOH A:2219
BINDING SITE FOR RESIDUE EDO A1295
16
BC7
SOFTWARE
ARG A:95 , LYS A:149 , ALA A:150 , LYS A:151 , LEU A:152 , PRO A:153 , HOH A:2113
BINDING SITE FOR RESIDUE EDO A1296
17
BC8
SOFTWARE
LEU A:29 , LYS A:32 , ARG A:158 , EDO A:1291 , HOH A:2037 , HOH A:2162 , HOH A:2241
BINDING SITE FOR RESIDUE SO4 A1297
18
BC9
SOFTWARE
ARG A:47 , HIS A:87 , PHE A:88 , HOH A:2101 , HOH A:2117 , HOH A:2243 , HIS B:87 , ARG B:105
BINDING SITE FOR RESIDUE SO4 A1298
19
CC1
SOFTWARE
LYS B:18 , HIS B:19 , THR B:41 , HIS B:42 , ALA B:43 , GLY B:44 , GLY B:99 , SER B:100 , GLU B:118 , LEU B:119 , HIS B:120 , ALA B:142 , ASP B:143 , GLY B:144 , ASP B:164 , HOH B:2016 , HOH B:2038 , HOH B:2039 , HOH B:2094
BINDING SITE FOR RESIDUE SAM B1281
20
CC2
SOFTWARE
MET B:169 , THR B:171 , ASP B:172 , EDO B:1286
BINDING SITE FOR RESIDUE PEG B1282
21
CC3
SOFTWARE
ARG B:201 , ILE B:208 , GLN B:221 , EDO B:1296 , HOH B:2139 , HOH B:2188 , HOH B:2189
BINDING SITE FOR RESIDUE EDO B1283
22
CC4
SOFTWARE
PRO B:228 , ASP B:229 , GLY B:270 , HIS B:271 , HOH B:2140 , HOH B:2190
BINDING SITE FOR RESIDUE EDO B1284
23
CC5
SOFTWARE
ALA B:66 , TRP B:69 , EDO B:1289 , HOH B:2132 , HOH B:2191
BINDING SITE FOR RESIDUE EDO B1285
24
CC6
SOFTWARE
PHE B:145 , PRO B:165 , PRO B:166 , ASP B:172 , PEG B:1282 , HOH B:2037
BINDING SITE FOR RESIDUE EDO B1286
25
CC7
SOFTWARE
THR B:214 , GLY B:215 , ILE B:216 , HOH B:2060 , HOH B:2147
BINDING SITE FOR RESIDUE EDO B1287
26
CC8
SOFTWARE
ARG B:158
BINDING SITE FOR RESIDUE EDO B1288
27
CC9
SOFTWARE
TYR B:61 , LEU B:62 , ALA B:66 , LEU B:94 , PRO B:153 , ARG B:186 , EDO B:1285 , HOH B:2049 , HOH B:2051
BINDING SITE FOR RESIDUE EDO B1289
28
DC1
SOFTWARE
TRP B:247 , GLU B:250 , TRP B:276 , HOH B:2164
BINDING SITE FOR RESIDUE EDO B1290
29
DC2
SOFTWARE
ALA B:76 , GLU B:77 , GLU B:79 , ALA B:80 , HOH B:2020
BINDING SITE FOR RESIDUE EDO B1291
30
DC3
SOFTWARE
HIS B:261 , SER B:262 , VAL B:265 , GLY B:268 , HOH B:2179 , HOH B:2193
BINDING SITE FOR RESIDUE EDO B1292
31
DC4
SOFTWARE
PHE B:145 , LYS B:149 , SER B:178 , GLY B:179 , GLU B:182 , HOH B:2122 , HOH B:2194
BINDING SITE FOR RESIDUE EDO B1293
32
DC5
SOFTWARE
ALA B:181 , THR B:214 , HOH B:2124
BINDING SITE FOR RESIDUE EDO B1294
33
DC6
SOFTWARE
ASN B:255
BINDING SITE FOR RESIDUE EDO B1295
34
DC7
SOFTWARE
HOH A:2170 , ILE B:208 , GLU B:212 , GLN B:221 , EDO B:1283 , HOH B:2188 , HOH B:2189
BINDING SITE FOR RESIDUE EDO B1296
[
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, 4)
Info
All PROSITE Patterns/Profiles
1: N6_MTASE (A:161-167,B:161-167|A:241-247,B:24...)
;
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
4
A:161-167
B:161-167
A:241-247
B:241-247
[
close PROSITE info
]
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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d4blva_ (A:)
1b: SCOP_d4blvb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d4blva_
A:
1b
d4blvb_
B:
[
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
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
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)
[
close Script example commands
]
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") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (114 KB)
Header - Asym.Unit
Biol.Unit 1 (56 KB)
Header - Biol.Unit 1
Biol.Unit 2 (55 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
4BLV
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help