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.
4BH5
Asym. Unit
Info
Asym.Unit (95 KB)
Biol.Unit 1 (25 KB)
Biol.Unit 2 (25 KB)
Biol.Unit 3 (25 KB)
Biol.Unit 4 (25 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
LYTM DOMAIN OF ENVC, AN ACTIVATOR OF CELL WALL AMIDASES IN ESCHERICHIA COLI
Authors
:
C. Morlot, N. T. Peters, D. C. Yang, T. Uehara, T. Vernet, T. G. Bernhardt
Date
:
29 Mar 13 (Deposition) - 03 Jul 13 (Release) - 28 Aug 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.57
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Cell Cycle, Amidase Activator, Autolysin, Cytokinesis, Morphogenesis, Sacculus, Peptidoglycan
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. T. Peters, C. Morlot, D. C. Yang, T. Uehara, T. Vernet, T. G. Bernhard
Structure-Function Analysis Of The Lytm Domain Of Envc, An Activator Of Cell Wall Remodeling At The Escherichia Coli Division Site.
Mol. Microbiol. V. 89 690 2013
[
close entry info
]
Hetero Components
(4, 30)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: IODIDE ION (IODa)
3b: IODIDE ION (IODb)
3c: IODIDE ION (IODc)
3d: IODIDE ION (IODd)
3e: IODIDE ION (IODe)
3f: IODIDE ION (IODf)
3g: IODIDE ION (IODg)
3h: IODIDE ION (IODh)
3i: IODIDE ION (IODi)
3j: IODIDE ION (IODj)
3k: IODIDE ION (IODk)
3l: IODIDE ION (IODl)
3m: IODIDE ION (IODm)
3n: IODIDE ION (IODn)
3o: IODIDE ION (IODo)
3p: IODIDE ION (IODp)
3q: IODIDE ION (IODq)
3r: IODIDE ION (IODr)
3s: IODIDE ION (IODs)
3t: IODIDE ION (IODt)
3u: IODIDE ION (IODu)
3v: IODIDE ION (IODv)
3w: IODIDE ION (IODw)
4a: POTASSIUM ION (Ka)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
4
Ligand/Ion
CHLORIDE ION
2
GOL
2
Ligand/Ion
GLYCEROL
3
IOD
23
Ligand/Ion
IODIDE ION
4
K
1
Ligand/Ion
POTASSIUM ION
[
close Hetero Component info
]
Sites
(28, 28)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:410 , ARG D:405
BINDING SITE FOR RESIDUE IOD A1420
02
AC2
SOFTWARE
IOD B:1421
BINDING SITE FOR RESIDUE IOD A1421
03
AC3
SOFTWARE
GLN A:348 , HOH D:2045
BINDING SITE FOR RESIDUE IOD A1422
04
AC4
SOFTWARE
GLY A:339 , ARG A:340
BINDING SITE FOR RESIDUE IOD A1423
05
AC5
SOFTWARE
TRP A:346 , GLY A:349 , GLY A:351
BINDING SITE FOR RESIDUE CL A1424
06
AC6
SOFTWARE
IOD B:1500
BINDING SITE FOR RESIDUE IOD B1420
07
AC7
SOFTWARE
IOD A:1421 , ALA B:293 , ARG B:406
BINDING SITE FOR RESIDUE IOD B1421
08
AC8
SOFTWARE
ALA B:410 , ARG C:405
BINDING SITE FOR RESIDUE IOD B1422
09
AC9
SOFTWARE
GLN B:379
BINDING SITE FOR RESIDUE IOD B1423
10
BC1
SOFTWARE
TRP B:346 , GLN B:348 , GLY B:349 , GLY B:351
BINDING SITE FOR RESIDUE CL B1424
11
BC2
SOFTWARE
ALA A:293 , ARG A:406 , IOD B:1420
BINDING SITE FOR RESIDUE IOD B1500
12
BC3
SOFTWARE
TRP D:300
BINDING SITE FOR RESIDUE IOD B1501
13
BC4
SOFTWARE
GLN C:313 , GLY C:316
BINDING SITE FOR RESIDUE IOD B1503
14
BC5
SOFTWARE
ALA C:293 , ARG C:406 , IOD D:1420
BINDING SITE FOR RESIDUE IOD C1420
15
BC6
SOFTWARE
SER C:391 , IOD C:1500
BINDING SITE FOR RESIDUE IOD C1421
16
BC7
SOFTWARE
GLN B:348
BINDING SITE FOR RESIDUE IOD C1422
17
BC8
SOFTWARE
SER C:328 , GLU C:329
BINDING SITE FOR RESIDUE IOD C1423
18
BC9
SOFTWARE
HOH C:2013
BINDING SITE FOR RESIDUE IOD C1424
19
CC1
SOFTWARE
TRP C:346 , GLN C:348 , GLY C:349 , GLY C:351 , SER C:392
BINDING SITE FOR RESIDUE CL C1425
20
CC2
SOFTWARE
GLN B:407 , GLY B:408 , LYS C:321 , TYR C:350 , GLU C:403 , ARG C:405
BINDING SITE FOR RESIDUE GOL C1426
21
CC3
SOFTWARE
IOD C:1421 , ARG D:406
BINDING SITE FOR RESIDUE IOD C1500
22
CC4
SOFTWARE
IOD C:1420 , SER D:391 , SER D:392
BINDING SITE FOR RESIDUE IOD D1420
23
CC5
SOFTWARE
GLN D:313 , GLY D:316
BINDING SITE FOR RESIDUE IOD D1421
24
CC6
SOFTWARE
ARG B:340 , THR D:306
BINDING SITE FOR RESIDUE IOD D1422
25
CC7
SOFTWARE
HOH B:2027 , SER D:328 , GLU D:329
BINDING SITE FOR RESIDUE IOD D1423
26
CC8
SOFTWARE
TRP D:346 , GLN D:348 , GLY D:349 , GLY D:351 , SER D:392
BINDING SITE FOR RESIDUE CL D1424
27
CC9
SOFTWARE
GLN A:407 , GLY A:408 , HOH A:2111 , LYS D:321 , TYR D:350 , GLU D:403 , ARG D:405 , HOH D:2080
BINDING SITE FOR RESIDUE GOL D1425
28
DC1
SOFTWARE
GLN A:348
BINDING SITE FOR RESIDUE IOD D1500
[
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
Chain C
Chain D
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 (95 KB)
Header - Asym.Unit
Biol.Unit 1 (25 KB)
Header - Biol.Unit 1
Biol.Unit 2 (25 KB)
Header - Biol.Unit 2
Biol.Unit 3 (25 KB)
Header - Biol.Unit 3
Biol.Unit 4 (25 KB)
Header - Biol.Unit 4
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
4BH5
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
