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.
2XZW
Asym. Unit
Info
Asym.Unit (325 KB)
Biol.Unit 1 (110 KB)
Biol.Unit 2 (104 KB)
Biol.Unit 3 (109 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF PII FROM SYNECHOCOCCUS ELONGATUS IN COMPLEX WITH 2-OXOGLUTARATE AT LOW 2-OG CONCENTRATIONS
Authors
:
K. Zeth, V. -R. Chellamuthu, K. Forchhammer, O. Fokina
Date
:
29 Nov 10 (Deposition) - 08 Dec 10 (Release) - 08 Dec 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Biol. Unit 3: G,H,I (1x)
Keywords
:
Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
O. Fokina, V. -R. Chellamuthu, K. Forchhammer, K. Zeth
Mechanism Of 2-Oxoglutarate Signaling By The Synechococcus Elongatus Pii Signal Transduction Protein.
Proc. Natl. Acad. Sci. Usa V. 107 19760 2010
[
close entry info
]
Hetero Components
(3, 21)
Info
All Hetero Components
1a: 2-OXOGLUTARIC ACID (AKGa)
1b: 2-OXOGLUTARIC ACID (AKGb)
1c: 2-OXOGLUTARIC ACID (AKGc)
1d: 2-OXOGLUTARIC ACID (AKGd)
1e: 2-OXOGLUTARIC ACID (AKGe)
1f: 2-OXOGLUTARIC ACID (AKGf)
2a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
2b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2c: ADENOSINE-5'-TRIPHOSPHATE (ATPc)
2d: ADENOSINE-5'-TRIPHOSPHATE (ATPd)
2e: ADENOSINE-5'-TRIPHOSPHATE (ATPe)
2f: ADENOSINE-5'-TRIPHOSPHATE (ATPf)
2g: ADENOSINE-5'-TRIPHOSPHATE (ATPg)
2h: ADENOSINE-5'-TRIPHOSPHATE (ATPh)
2i: ADENOSINE-5'-TRIPHOSPHATE (ATPi)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AKG
6
Ligand/Ion
2-OXOGLUTARIC ACID
2
ATP
9
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
3
MG
6
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ILE A:7 , GLY A:35 , PHE A:36 , GLY A:37 , ARG A:38 , GLN A:39 , LYS A:58 , ILE A:86 , GLY A:87 , ASP A:88 , GLY A:89 , LYS A:90 , AKG A:201 , MG A:202 , HOH A:2025 , HOH A:2026 , GLY B:27 , MET B:28 , THR B:29 , GLU B:62 , VAL B:64 , ARG B:101 , ARG B:103 , HOH B:2037
BINDING SITE FOR RESIDUE ATP A 200
02
AC2
SOFTWARE
ARG A:9 , GLY A:37 , ARG A:38 , GLN A:39 , LYS A:40 , GLY A:41 , LEU A:56 , LYS A:58 , GLY A:87 , ATP A:200 , MG A:202 , HOH A:2026
BINDING SITE FOR RESIDUE AKG A 201
03
AC3
SOFTWARE
GLN A:39 , ATP A:200 , AKG A:201
BINDING SITE FOR RESIDUE MG A 202
04
AC4
SOFTWARE
ILE B:7 , GLY B:35 , PHE B:36 , ARG B:38 , GLN B:39 , LYS B:58 , ILE B:86 , GLY B:87 , ASP B:88 , GLY B:89 , LYS B:90 , AKG B:201 , MG B:202 , HOH B:2042 , HOH B:2043 , HOH B:2045 , GLY C:27 , MET C:28 , THR C:29 , GLU C:62 , ILE C:63 , VAL C:64 , ARG C:101 , ARG C:103
BINDING SITE FOR RESIDUE ATP B 200
05
AC5
SOFTWARE
ARG B:9 , PHE B:36 , GLY B:37 , ARG B:38 , GLN B:39 , LYS B:40 , GLY B:41 , LEU B:56 , LYS B:58 , ILE B:86 , GLY B:87 , ATP B:200 , MG B:202 , HOH B:2044 , HOH B:2045
BINDING SITE FOR RESIDUE AKG B 201
06
AC6
SOFTWARE
GLN B:39 , ATP B:200 , AKG B:201
BINDING SITE FOR RESIDUE MG B 202
07
AC7
SOFTWARE
GLY A:27 , MET A:28 , THR A:29 , GLU A:62 , VAL A:64 , ARG A:101 , ARG A:103 , HOH A:2023 , ILE C:7 , GLY C:35 , PHE C:36 , GLY C:37 , ARG C:38 , GLN C:39 , LYS C:58 , ILE C:86 , GLY C:87 , ASP C:88 , GLY C:89 , LYS C:90 , AKG C:201 , MG C:202 , HOH C:2040 , HOH C:2041
BINDING SITE FOR RESIDUE ATP C 200
08
AC8
SOFTWARE
ARG C:9 , PHE C:36 , GLY C:37 , ARG C:38 , GLN C:39 , LYS C:40 , GLY C:41 , LEU C:56 , LYS C:58 , ILE C:86 , GLY C:87 , ATP C:200 , MG C:202 , HOH C:2040 , HOH C:2042
BINDING SITE FOR RESIDUE AKG C 201
09
AC9
SOFTWARE
GLN C:39 , ATP C:200 , AKG C:201
BINDING SITE FOR RESIDUE MG C 202
10
BC1
SOFTWARE
ILE D:7 , GLY D:35 , PHE D:36 , GLY D:37 , ARG D:38 , GLN D:39 , ILE D:86 , GLY D:87 , ASP D:88 , GLY D:89 , LYS D:90 , HOH D:2039 , HOH D:2040 , GLY E:27 , MET E:28 , THR E:29 , GLU E:62 , ILE E:63 , VAL E:64 , ARG E:101 , ARG E:103
BINDING SITE FOR RESIDUE ATP D 200
11
BC2
SOFTWARE
ILE E:7 , GLY E:35 , PHE E:36 , GLY E:37 , ARG E:38 , LYS E:58 , ILE E:86 , GLY E:87 , ASP E:88 , GLY E:89 , LYS E:90 , HOH E:2037 , GLY F:27 , MET F:28 , THR F:29 , GLU F:62 , ILE F:63 , VAL F:64 , ARG F:101 , ARG F:103 , ILE F:112
BINDING SITE FOR RESIDUE ATP E 200
12
BC3
SOFTWARE
GLY D:27 , MET D:28 , THR D:29 , GLU D:62 , ILE D:63 , VAL D:64 , ARG D:101 , ARG D:103 , ILE F:7 , GLY F:35 , PHE F:36 , GLY F:37 , ARG F:38 , GLN F:39 , LYS F:58 , ILE F:86 , GLY F:87 , ASP F:88 , GLY F:89 , LYS F:90 , AKG F:201 , MG F:202 , HOH F:2035 , HOH F:2036 , HOH F:2037
BINDING SITE FOR RESIDUE ATP F 200
13
BC4
SOFTWARE
ARG F:9 , PHE F:36 , GLY F:37 , ARG F:38 , GLN F:39 , LYS F:40 , GLY F:41 , THR F:43 , LEU F:56 , LYS F:58 , ILE F:86 , GLY F:87 , ATP F:200 , MG F:202 , HOH F:2037 , HOH F:2038
BINDING SITE FOR RESIDUE AKG F 201
14
BC5
SOFTWARE
GLN F:39 , ATP F:200 , AKG F:201
BINDING SITE FOR RESIDUE MG F 202
15
BC6
SOFTWARE
ILE G:7 , GLY G:35 , PHE G:36 , GLY G:37 , ARG G:38 , GLN G:39 , LYS G:58 , GLY G:87 , GLY G:89 , LYS G:90 , HOH G:2024 , GLY H:27 , MET H:28 , THR H:29 , GLU H:62 , ILE H:63 , VAL H:64 , ARG H:101 , ARG H:103
BINDING SITE FOR RESIDUE ATP G 200
16
BC7
SOFTWARE
ILE H:7 , GLY H:35 , PHE H:36 , ARG H:38 , GLN H:39 , ILE H:86 , GLY H:87 , ASP H:88 , GLY H:89 , LYS H:90 , AKG H:201 , MG H:202 , HOH H:2026 , HOH H:2027 , VAL I:26 , GLY I:27 , MET I:28 , THR I:29 , GLU I:62 , VAL I:64 , ARG I:101 , ARG I:103
BINDING SITE FOR RESIDUE ATP H 200
17
BC8
SOFTWARE
ARG H:9 , GLY H:37 , ARG H:38 , GLN H:39 , LYS H:40 , GLY H:41 , GLN H:42 , LEU H:56 , LYS H:58 , ILE H:86 , GLY H:87 , ATP H:200 , MG H:202 , HOH H:2026
BINDING SITE FOR RESIDUE AKG H 201
18
BC9
SOFTWARE
GLN H:39 , ATP H:200 , AKG H:201
BINDING SITE FOR RESIDUE MG H 202
19
CC1
SOFTWARE
GLY G:27 , MET G:28 , THR G:29 , GLU G:62 , VAL G:64 , ARG G:101 , ARG G:103 , ILE I:7 , GLY I:35 , PHE I:36 , GLY I:37 , ARG I:38 , GLN I:39 , ILE I:86 , GLY I:87 , ASP I:88 , GLY I:89 , LYS I:90 , AKG I:201 , MG I:202 , HOH I:2037 , HOH I:2038
BINDING SITE FOR RESIDUE ATP I 200
20
CC2
SOFTWARE
ARG I:9 , GLY I:37 , ARG I:38 , GLN I:39 , LYS I:40 , GLY I:41 , THR I:43 , LEU I:56 , LYS I:58 , ILE I:86 , GLY I:87 , ATP I:200 , MG I:202 , HOH I:2038 , HOH I:2039
BINDING SITE FOR RESIDUE AKG I 201
21
CC3
SOFTWARE
GLN I:39 , GLY I:87 , ATP I:200 , AKG I:201
BINDING SITE FOR RESIDUE MG I 202
[
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, 25)
Info
All PROSITE Patterns/Profiles
1: PII_GLNB_DOM (A:1-112,B:1-112,C:1-112,D:1-112,E:...)
2: PII_GLNB_UMP (A:51-51,B:50-51,C:46-51,F:46-46,G:...)
3: PII_GLNB_CTER (A:83-96,B:83-96,C:83-96,D:83-96,E:...)
;
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
9
A:1-112
B:1-112
C:1-112
D:1-112
E:1-111
F:1-112
G:1-112
H:1-109
I:1-109
2
PII_GLNB_UMP
PS00496
P-II protein uridylation site.
GLNB_SYNE7
46-51
7
A:51-51
B:50-51
C:46-51
F:46-46
G:50-51
H:46-51
I:46-46
3
PII_GLNB_CTER
PS00638
P-II protein C-terminal region signature.
GLNB_SYNE7
83-96
9
A:83-96
B:83-96
C:83-96
D:83-96
E:83-96
F:83-96
G:83-96
H:83-96
I: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.
SCOP Domains
(1, 9)
Info
All SCOP Domains
1a: SCOP_d2xzwa_ (A:)
1b: SCOP_d2xzwb_ (B:)
1c: SCOP_d2xzwc_ (C:)
1d: SCOP_d2xzwd_ (D:)
1e: SCOP_d2xzwe_ (E:)
1f: SCOP_d2xzwf_ (F:)
1g: SCOP_d2xzwg_ (G:)
1h: SCOP_d2xzwh_ (H:)
1i: SCOP_d2xzwi_ (I:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
GlnB-like
(79)
Family
:
Prokaryotic signal transducing protein
(31)
Protein domain
:
automated matches
(9)
Synechococcus elongatus PCC 7942 [TaxId: 1140]
(3)
1a
d2xzwa_
A:
1b
d2xzwb_
B:
1c
d2xzwc_
C:
1d
d2xzwd_
D:
1e
d2xzwe_
E:
1f
d2xzwf_
F:
1g
d2xzwg_
G:
1h
d2xzwh_
H:
1i
d2xzwi_
I:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 9)
Info
all PFAM domains
1a: PFAM_P_II_2xzwI01 (I:4-105)
1b: PFAM_P_II_2xzwI02 (I:4-105)
1c: PFAM_P_II_2xzwI03 (I:4-105)
1d: PFAM_P_II_2xzwI04 (I:4-105)
1e: PFAM_P_II_2xzwI05 (I:4-105)
1f: PFAM_P_II_2xzwI06 (I:4-105)
1g: PFAM_P_II_2xzwI07 (I:4-105)
1h: PFAM_P_II_2xzwI08 (I:4-105)
1i: PFAM_P_II_2xzwI09 (I:4-105)
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-2xzwI01
I:4-105
1b
P-II-2xzwI02
I:4-105
1c
P-II-2xzwI03
I:4-105
1d
P-II-2xzwI04
I:4-105
1e
P-II-2xzwI05
I:4-105
1f
P-II-2xzwI06
I:4-105
1g
P-II-2xzwI07
I:4-105
1h
P-II-2xzwI08
I:4-105
1i
P-II-2xzwI09
I:4-105
[
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
Chain G
Chain H
Chain I
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 (325 KB)
Header - Asym.Unit
Biol.Unit 1 (110 KB)
Header - Biol.Unit 1
Biol.Unit 2 (104 KB)
Header - Biol.Unit 2
Biol.Unit 3 (109 KB)
Header - Biol.Unit 3
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
2XZW
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
