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.
4Y1M
Asym. Unit
Info
Asym.Unit (186 KB)
Biol.Unit 1 (106 KB)
Biol.Unit 2 (76 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
AN ESCHERICHIA COLI YYBP-YKOY MN RIBOSWITCH IN THE MN2+-FREE STATE
Authors
:
I. R. Price, A. Ke
Date
:
08 Feb 15 (Deposition) - 08 Apr 15 (Release) - 20 Jul 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: B (1x)
Biol. Unit 2: A (1x)
Keywords
:
Riboswitch, Manganese, Free State, Rna
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. R. Price, A. Gaballa, F. Ding, J. D. Helmann, A. Ke
Mn(2+)-Sensing Mechanisms Of Yybp-Ykoy Orphan Riboswitches.
Mol. Cell V. 57 1110 2015
[
close entry info
]
Hetero Components
(3, 76)
Info
All Hetero Components
1a: GUANOSINE-5'-TRIPHOSPHATE (GTPa)
1b: GUANOSINE-5'-TRIPHOSPHATE (GTPb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
2i: MAGNESIUM ION (MGi)
3a: STRONTIUM ION (SRa)
3aa: STRONTIUM ION (SRaa)
3ab: STRONTIUM ION (SRab)
3ac: STRONTIUM ION (SRac)
3ad: STRONTIUM ION (SRad)
3ae: STRONTIUM ION (SRae)
3af: STRONTIUM ION (SRaf)
3ag: STRONTIUM ION (SRag)
3ah: STRONTIUM ION (SRah)
3ai: STRONTIUM ION (SRai)
3aj: STRONTIUM ION (SRaj)
3ak: STRONTIUM ION (SRak)
3al: STRONTIUM ION (SRal)
3am: STRONTIUM ION (SRam)
3an: STRONTIUM ION (SRan)
3ao: STRONTIUM ION (SRao)
3ap: STRONTIUM ION (SRap)
3aq: STRONTIUM ION (SRaq)
3ar: STRONTIUM ION (SRar)
3as: STRONTIUM ION (SRas)
3at: STRONTIUM ION (SRat)
3au: STRONTIUM ION (SRau)
3av: STRONTIUM ION (SRav)
3aw: STRONTIUM ION (SRaw)
3ax: STRONTIUM ION (SRax)
3ay: STRONTIUM ION (SRay)
3az: STRONTIUM ION (SRaz)
3b: STRONTIUM ION (SRb)
3ba: STRONTIUM ION (SRba)
3bb: STRONTIUM ION (SRbb)
3bc: STRONTIUM ION (SRbc)
3bd: STRONTIUM ION (SRbd)
3be: STRONTIUM ION (SRbe)
3bf: STRONTIUM ION (SRbf)
3bg: STRONTIUM ION (SRbg)
3bh: STRONTIUM ION (SRbh)
3bi: STRONTIUM ION (SRbi)
3bj: STRONTIUM ION (SRbj)
3bk: STRONTIUM ION (SRbk)
3bl: STRONTIUM ION (SRbl)
3bm: STRONTIUM ION (SRbm)
3c: STRONTIUM ION (SRc)
3d: STRONTIUM ION (SRd)
3e: STRONTIUM ION (SRe)
3f: STRONTIUM ION (SRf)
3g: STRONTIUM ION (SRg)
3h: STRONTIUM ION (SRh)
3i: STRONTIUM ION (SRi)
3j: STRONTIUM ION (SRj)
3k: STRONTIUM ION (SRk)
3l: STRONTIUM ION (SRl)
3m: STRONTIUM ION (SRm)
3n: STRONTIUM ION (SRn)
3o: STRONTIUM ION (SRo)
3p: STRONTIUM ION (SRp)
3q: STRONTIUM ION (SRq)
3r: STRONTIUM ION (SRr)
3s: STRONTIUM ION (SRs)
3t: STRONTIUM ION (SRt)
3u: STRONTIUM ION (SRu)
3v: STRONTIUM ION (SRv)
3w: STRONTIUM ION (SRw)
3x: STRONTIUM ION (SRx)
3y: STRONTIUM ION (SRy)
3z: STRONTIUM ION (SRz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GTP
2
Ligand/Ion
GUANOSINE-5'-TRIPHOSPHATE
2
MG
9
Ligand/Ion
MAGNESIUM ION
3
SR
65
Ligand/Ion
STRONTIUM ION
[
close Hetero Component info
]
Sites
(47, 47)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
26: AE8 (SOFTWARE)
27: AE9 (SOFTWARE)
28: AF1 (SOFTWARE)
29: AF2 (SOFTWARE)
30: AF3 (SOFTWARE)
31: AF4 (SOFTWARE)
32: AF5 (SOFTWARE)
33: AF6 (SOFTWARE)
34: AF7 (SOFTWARE)
35: AF8 (SOFTWARE)
36: AF9 (SOFTWARE)
37: AG1 (SOFTWARE)
38: AG2 (SOFTWARE)
39: AG3 (SOFTWARE)
40: AG4 (SOFTWARE)
41: AG5 (SOFTWARE)
42: AG6 (SOFTWARE)
43: AG7 (SOFTWARE)
44: AG8 (SOFTWARE)
45: AG9 (SOFTWARE)
46: AH1 (SOFTWARE)
47: AH2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
G B:9 , G B:10 , A B:11 , A B:45 , U B:49
binding site for residue SR B 201
02
AC2
SOFTWARE
G B:25 , HOH B:337
binding site for residue SR B 202
03
AC3
SOFTWARE
U B:34 , HOH B:345
binding site for residue SR B 203
04
AC4
SOFTWARE
U B:42 , G B:65 , HOH B:311
binding site for residue SR B 204
05
AC5
SOFTWARE
G B:9 , HOH B:315
binding site for residue SR B 205
06
AC6
SOFTWARE
G B:10 , C B:46 , U B:48
binding site for residue SR B 206
07
AC7
SOFTWARE
G B:94
binding site for residue SR B 208
08
AC8
SOFTWARE
HOH B:307 , HOH B:335
binding site for residue SR B 210
09
AC9
SOFTWARE
A B:76 , C B:77 , HOH B:325
binding site for residue MG B 211
10
AD1
SOFTWARE
C A:108 , GTP A:208 , G B:2 , A B:26 , C B:108
binding site for residue GTP B 212
11
AD2
SOFTWARE
A B:45 , C B:46 , HOH B:301
binding site for residue SR B 213
12
AD3
SOFTWARE
G B:12 , G B:97
binding site for residue SR B 214
13
AD4
SOFTWARE
U B:51
binding site for residue SR B 215
14
AD5
SOFTWARE
G B:56
binding site for residue SR B 216
15
AD6
SOFTWARE
HOH B:323 , HOH B:338 , HOH B:353
binding site for residue SR B 218
16
AD7
SOFTWARE
C B:46
binding site for residue SR B 219
17
AD8
SOFTWARE
HOH B:349
binding site for residue SR B 222
18
AD9
SOFTWARE
U B:106 , HOH B:308
binding site for residue SR B 223
19
AE1
SOFTWARE
HOH B:342 , HOH B:343
binding site for residue SR B 225
20
AE2
SOFTWARE
G B:74
binding site for residue SR B 228
21
AE3
SOFTWARE
G B:65
binding site for residue SR B 229
22
AE4
SOFTWARE
A B:57
binding site for residue SR B 233
23
AE5
SOFTWARE
HOH B:355
binding site for residue SR B 238
24
AE6
SOFTWARE
HOH B:350
binding site for residue SR B 239
25
AE7
SOFTWARE
HOH A:305
binding site for residue SR B 240
26
AE8
SOFTWARE
HOH B:339 , HOH B:348
binding site for residue SR B 243
27
AE9
SOFTWARE
G B:82 , HOH B:314 , HOH B:319 , HOH B:351
binding site for residue SR B 244
28
AF1
SOFTWARE
G B:18
binding site for residue SR B 245
29
AF2
SOFTWARE
C B:107
binding site for residue MG B 246
30
AF3
SOFTWARE
U A:42 , G A:65
binding site for residue SR A 201
31
AF4
SOFTWARE
G A:56 , HOH A:308
binding site for residue SR A 203
32
AF5
SOFTWARE
U A:104
binding site for residue SR A 204
33
AF6
SOFTWARE
A A:93 , G A:94
binding site for residue SR A 205
34
AF7
SOFTWARE
A A:44
binding site for residue SR A 207
35
AF8
SOFTWARE
G A:2 , C A:108 , C B:108 , GTP B:212 , HOH B:360
binding site for residue GTP A 208
36
AF9
SOFTWARE
G A:9 , G A:10 , A A:11 , A A:45
binding site for residue SR A 209
37
AG1
SOFTWARE
A A:44
binding site for residue SR A 212
38
AG2
SOFTWARE
G A:9
binding site for residue SR A 214
39
AG3
SOFTWARE
A A:45 , C A:46 , A A:47
binding site for residue SR A 215
40
AG4
SOFTWARE
U A:4
binding site for residue SR A 216
41
AG5
SOFTWARE
G A:56
binding site for residue SR A 217
42
AG6
SOFTWARE
U A:71 , HOH A:301 , HOH A:309
binding site for residue SR A 218
43
AG7
SOFTWARE
G A:12 , G A:97
binding site for residue SR A 219
44
AG8
SOFTWARE
U A:51
binding site for residue SR A 220
45
AG9
SOFTWARE
C A:46
binding site for residue SR A 221
46
AH1
SOFTWARE
C A:46
binding site for residue SR A 222
47
AH2
SOFTWARE
U A:64
binding site for residue MG A 225
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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
(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
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 (186 KB)
Header - Asym.Unit
Biol.Unit 1 (106 KB)
Header - Biol.Unit 1
Biol.Unit 2 (76 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
4Y1M
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
