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.
2JJ4
Biol. Unit 1
Info
Asym.Unit (180 KB)
Biol.Unit 1 (337 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE COMPLEX OF PII AND ACETYLGLUTAMATE KINASE FROM SYNECHOCOCCUS ELONGATUS PCC7942
Authors
:
J. L. Llacer, C. Marco-Marin, F. Gil-Ortiz, I. Fita, V. Rubio
Date
:
04 Jul 07 (Deposition) - 16 Oct 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.46
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (2x)
Keywords
:
Transferase, Cyanobacteria, Transcription, Acetylglutamate, Phosphorylation, Pii Signal Protein, Transcription Regulation, N-Acetyl-L-Glutamate Kinase, Nucleotide-Binding, Arginine Inhibition, Arginine Biosynthesis, Amino-Acid Biosynthesis, Glnb, Kinase, Trimer, Hexamer, Atp-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. L. Llacer, A. Contreras, K. Forchhammer, C. Marco-Marin, F. Gil-Ortiz, R. Maldonado, I. Fita, V. Rubio
The Crystal Structure Of The Complex Of Pii And Acetylglutamate Kinase Reveals How Pii Controls The Storage Of Nitrogen As Arginine
Proc. Nat. Acad. Sci. Usa V. 104 17644 2007
[
close entry info
]
Hetero Components
(1, 4)
Info
All Hetero Components
1a: N-ACETYL-L-GLUTAMATE (NLGa)
1b: N-ACETYL-L-GLUTAMATE (NLGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NLG
4
Ligand/Ion
N-ACETYL-L-GLUTAMATE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:69 , GLY A:70 , GLY A:71 , ILE A:74 , LEU A:91 , ARG A:92 , SER A:174 , ASN A:185 , ALA A:188
BINDING SITE FOR RESIDUE NLG A1292
2
AC2
SOFTWARE
GLY B:69 , GLY B:70 , GLY B:71 , ILE B:74 , GLY B:90 , LEU B:91 , ARG B:92 , ASN B:185 , ALA B:188
BINDING SITE FOR RESIDUE NLG B1292
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 18)
Info
All PROSITE Patterns/Profiles
1: PII_GLNB_DOM (D:1-111,E:1-108,F:1-109)
2: PII_GLNB_UMP (D:46-51,E:46-51,F:46-51)
3: PII_GLNB_CTER (D:83-96,E:83-96,F:83-96)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PII_GLNB_DOM
PS51343
P-II protein family profile.
GLNB_SYNE7
1-112
6
D:1-111
E:1-108
F:1-109
2
PII_GLNB_UMP
PS00496
P-II protein uridylation site.
GLNB_SYNE7
46-51
6
D:46-51
E:46-51
F:46-51
3
PII_GLNB_CTER
PS00638
P-II protein C-terminal region signature.
GLNB_SYNE7
83-96
6
D:83-96
E:83-96
F:83-96
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_2jj4E00 (E:1-108)
1b: CATH_2jj4F00 (F:1-109)
1c: CATH_2jj4D00 (D:1-111)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.120, no name defined]
(37)
Synechococcus elongatus. Organism_taxid: 1140. Strain: pcc 7942.
(4)
1a
2jj4E00
E:1-108
1b
2jj4F00
F:1-109
1c
2jj4D00
D:1-111
[
close CATH info
]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_P_II_2jj4F01 (F:4-105)
1b: PFAM_P_II_2jj4F02 (F:4-105)
1c: PFAM_P_II_2jj4F03 (F:4-105)
2a: PFAM_AA_kinase_2jj4C01 (C:30-267)
2b: PFAM_AA_kinase_2jj4C02 (C:30-267)
2c: PFAM_AA_kinase_2jj4C03 (C:30-267)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GlnB-like
(50)
Family
:
P-II
(26)
Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)
(7)
1a
P-II-2jj4F01
F:4-105
1b
P-II-2jj4F02
F:4-105
1c
P-II-2jj4F03
F:4-105
Clan
:
no clan defined [family: AA_kinase]
(20)
Family
:
AA_kinase
(20)
Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)
(2)
2a
AA_kinase-2jj4C01
C:30-267
2b
AA_kinase-2jj4C02
C:30-267
2c
AA_kinase-2jj4C03
C:30-267
[
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
Chain E
Chain F
Asymmetric Unit 1
Asymmetric Unit 2
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 (180 KB)
Header - Asym.Unit
Biol.Unit 1 (337 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
2JJ4
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
