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.
1U12
Asym. Unit
Info
Asym.Unit (45 KB)
Biol.Unit 1 (40 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
M. LOTI CYCLIC NUCLEOTIDE BINDING DOMAIN MUTANT
Authors
:
G. M. Clayton, W. R. Silverman, L. Heginbotham, J. H. Morais-Cabral
Date
:
14 Jul 04 (Deposition) - 30 Nov 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Mutant Cyclic Nucleotide Binding Domain, C-Helix Mutation, Unliganded, Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. M. Clayton, W. R. Silverman, L. Heginbotham, J. H. Morais-Cabral
Structural Basis Of Ligand Activation In A Cyclic Nucleotid Regulated Potassium Channel
Cell(Cambridge, Mass. ) V. 119 615 2004
[
close entry info
]
Hetero Components
(3, 37)
Info
All Hetero Components
1a: IODIDE ION (IODa)
1aa: IODIDE ION (IODaa)
1ab: IODIDE ION (IODab)
1ac: IODIDE ION (IODac)
1ad: IODIDE ION (IODad)
1ae: IODIDE ION (IODae)
1b: IODIDE ION (IODb)
1c: IODIDE ION (IODc)
1d: IODIDE ION (IODd)
1e: IODIDE ION (IODe)
1f: IODIDE ION (IODf)
1g: IODIDE ION (IODg)
1h: IODIDE ION (IODh)
1i: IODIDE ION (IODi)
1j: IODIDE ION (IODj)
1k: IODIDE ION (IODk)
1l: IODIDE ION (IODl)
1m: IODIDE ION (IODm)
1n: IODIDE ION (IODn)
1o: IODIDE ION (IODo)
1p: IODIDE ION (IODp)
1q: IODIDE ION (IODq)
1r: IODIDE ION (IODr)
1s: IODIDE ION (IODs)
1t: IODIDE ION (IODt)
1u: IODIDE ION (IODu)
1v: IODIDE ION (IODv)
1w: IODIDE ION (IODw)
1x: IODIDE ION (IODx)
1y: IODIDE ION (IODy)
1z: IODIDE ION (IODz)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
2c: POTASSIUM ION (Kc)
2d: POTASSIUM ION (Kd)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
IOD
31
Ligand/Ion
IODIDE ION
2
K
4
Ligand/Ion
POTASSIUM ION
3
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(27, 27)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA B:242
BINDING SITE FOR RESIDUE IOD B 211
02
AC2
SOFTWARE
LYS A:238
BINDING SITE FOR RESIDUE IOD A 356
03
AC3
SOFTWARE
ARG A:271 , ARG B:307
BINDING SITE FOR RESIDUE IOD A 411
04
AC4
SOFTWARE
SER A:281 , PRO A:287
BINDING SITE FOR RESIDUE IOD A 511
05
AC5
SOFTWARE
ARG A:307 , ARG B:271
BINDING SITE FOR RESIDUE IOD A 611
06
AC6
SOFTWARE
PHE A:223 , ARG A:249
BINDING SITE FOR RESIDUE IOD A 711
07
AC7
SOFTWARE
LEU A:229
BINDING SITE FOR RESIDUE IOD A 811
08
AC8
SOFTWARE
PRO B:234
BINDING SITE FOR RESIDUE IOD B 911
09
AC9
SOFTWARE
GLY B:221
BINDING SITE FOR RESIDUE IOD B 112
10
BC1
SOFTWARE
PRO A:257 , THR B:255
BINDING SITE FOR RESIDUE IOD B 122
11
BC2
SOFTWARE
ALA A:325 , GLN A:328
BINDING SITE FOR RESIDUE IOD A 132
12
BC3
SOFTWARE
PRO A:234
BINDING SITE FOR RESIDUE IOD A 142
13
BC4
SOFTWARE
SER A:303
BINDING SITE FOR RESIDUE IOD A 192
14
BC5
SOFTWARE
THR A:255 , THR B:255
BINDING SITE FOR RESIDUE IOD B 212
15
BC6
SOFTWARE
GLU A:347
BINDING SITE FOR RESIDUE IOD A 812
16
BC7
SOFTWARE
PRO B:306
BINDING SITE FOR RESIDUE IOD B 913
17
BC8
SOFTWARE
PHE B:223 , IOD B:918
BINDING SITE FOR RESIDUE IOD B 914
18
BC9
SOFTWARE
HOH B:8
BINDING SITE FOR RESIDUE IOD B 915
19
CC1
SOFTWARE
SO4 A:145 , ARG A:254 , PHE B:273
BINDING SITE FOR RESIDUE IOD B 916
20
CC2
SOFTWARE
ARG B:249 , IOD B:914
BINDING SITE FOR RESIDUE IOD B 918
21
CC3
SOFTWARE
GLN B:328
BINDING SITE FOR RESIDUE IOD B 919
22
CC4
SOFTWARE
CYS A:263 , GLY A:297 , ARG A:307 , SER A:308 , ALA A:309 , K A:455
BINDING SITE FOR RESIDUE SO4 A 144
23
CC5
SOFTWARE
ARG A:254 , ARG A:271 , PHE A:273 , SER A:321 , ARG B:254 , ARG B:271 , IOD B:916
BINDING SITE FOR RESIDUE SO4 A 145
24
CC6
SOFTWARE
GLY A:291
BINDING SITE FOR RESIDUE K A 155
25
CC7
SOFTWARE
PRO B:287
BINDING SITE FOR RESIDUE K B 920
26
CC8
SOFTWARE
SER A:279
BINDING SITE FOR RESIDUE K A 814
27
CC9
SOFTWARE
SO4 A:144
BINDING SITE FOR RESIDUE K A 455
[
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
(3, 6)
Info
All PROSITE Patterns/Profiles
1: CNMP_BINDING_3 (A:235-347,B:235-347)
2: CNMP_BINDING_1 (A:262-278,B:262-278)
3: CNMP_BINDING_2 (A:296-313,B:296-313)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CNMP_BINDING_3
PS50042
cAMP/cGMP binding motif profile.
CNGK1_RHILO
235-348
2
A:235-347
B:235-347
2
CNMP_BINDING_1
PS00888
Cyclic nucleotide-binding domain signature 1.
CNGK1_RHILO
262-278
2
A:262-278
B:262-278
3
CNMP_BINDING_2
PS00889
Cyclic nucleotide-binding domain signature 2.
CNGK1_RHILO
296-313
2
A:296-313
B:296-313
[
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_d1u12a_ (A:)
1b: SCOP_d1u12b_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Double-stranded beta-helix
(580)
Superfamily
:
cAMP-binding domain-like
(99)
Family
:
cAMP-binding domain
(78)
Protein domain
:
Putative ion channel CnbD
(2)
Mesorhizobium loti [TaxId: 381]
(2)
1a
d1u12a_
A:
1b
d1u12b_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1u12A00 (A:219-349)
1b: CATH_1u12B00 (B:221-347)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
Jelly Rolls
(177)
Mesorhizobium loti maff303099. Organism_taxid: 266835. Strain: maff303099.
(1)
1a
1u12A00
A:219-349
1b
1u12B00
B:221-347
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_cNMP_binding_1u12B01 (B:253-336)
1b: PFAM_cNMP_binding_1u12B02 (B:253-336)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: cNMP_binding]
(41)
Family
:
cNMP_binding
(41)
Rhizobium loti (Mesorhizobium loti)
(4)
1a
cNMP_binding-1u12B01
B:253-336
1b
cNMP_binding-1u12B02
B:253-336
[
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 (45 KB)
Header - Asym.Unit
Biol.Unit 1 (40 KB)
Header - Biol.Unit 1
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
1U12
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help