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.
2J46
Asym. Unit
Info
Asym.Unit (457 KB)
Biol.Unit 1 (227 KB)
Biol.Unit 2 (227 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
WATER STRUCTURE OF T. AQUATICUS FFH NG DOMAIN AT 1.1A RESOLUTION
Authors
:
D. M. Freymann, U. D. Ramirez
Date
:
24 Aug 06 (Deposition) - 30 Nov 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.14
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Ribonucleoprotein, Nucleotide-Binding, Srp, Ffh, Water, Gtpase, Rna-Binding, Gtp-Binding, Signal Recognition Particle
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
U. D. Ramirez, D. M. Freymann
Analysis Of Protein Hydration In Ultra-High Resolution Structures Of The Srp Gtpase Ffh
Acta Crystallogr. , Sect. D V. 62 1520 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 10)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
3a: MANGANESE (II) ION (MNa)
3b: MANGANESE (II) ION (MNb)
4a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
4b: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
2
Ligand/Ion
ACETATE ION
2
CL
4
Ligand/Ion
CHLORIDE ION
3
MN
2
Ligand/Ion
MANGANESE (II) ION
4
MRD
2
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:109 , ASP A:219 , HOH A:2137 , HOH A:2248 , HOH A:2252
BINDING SITE FOR RESIDUE CL A1299
02
AC2
SOFTWARE
ALA A:133 , ALA A:134 , ASP A:135 , ALA A:141 , ARG A:142 , LEU A:145 , ASP A:187 , THR A:188
BINDING SITE FOR RESIDUE ACT A1300
03
AC3
SOFTWARE
GLN B:107 , ARG B:138 , LEU B:192
BINDING SITE FOR RESIDUE CL A1301
04
AC4
SOFTWARE
ARG A:138 , LEU A:192
BINDING SITE FOR RESIDUE CL A1302
05
AC5
SOFTWARE
GLU A:46 , GLU A:207 , HOH A:2310 , HOH A:2311 , HOH A:2312
BINDING SITE FOR RESIDUE MN A1400
06
AC6
SOFTWARE
LYS B:206 , ARG B:260 , HOH B:2182 , HOH B:2185 , HOH B:2218
BINDING SITE FOR RESIDUE CL B1298
07
AC7
SOFTWARE
ALA B:133 , ALA B:134 , ASP B:135 , ARG B:142 , LEU B:145 , ASP B:187 , THR B:188
BINDING SITE FOR RESIDUE ACT B1302
08
AC8
SOFTWARE
GLU B:46 , GLU B:207 , HOH B:2245 , HOH B:2246 , HOH B:2247
BINDING SITE FOR RESIDUE MN B1400
09
AC9
SOFTWARE
ALA A:81 , GLU A:84 , ARG A:169 , GLU A:207 , VAL A:208 , HOH A:2305 , HOH A:2306 , HOH A:2307 , HOH A:2308 , HOH A:2309
BINDING SITE FOR RESIDUE MRD A1297
10
BC1
SOFTWARE
GLU B:280 , PRO B:281 , TYR B:283 , ARG B:286 , LEU B:287 , ARG B:290 , HOH B:2244
BINDING SITE FOR RESIDUE MRD B1299
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: SRP54 (A:266-279,B:266-279)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SRP54
PS00300
SRP54-type proteins GTP-binding domain signature.
SRP54_THEAQ
266-279
2
A:266-279
B:266-279
[
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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2j46a1 (A:1-88)
1b: SCOP_d2j46b1 (B:1-88)
2a: SCOP_d2j46a2 (A:89-296)
2b: SCOP_d2j46b2 (B:89-297)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Four-helical up-and-down bundle
(308)
Superfamily
:
Domain of the SRP/SRP receptor G-proteins
(34)
Family
:
Domain of the SRP/SRP receptor G-proteins
(29)
Protein domain
:
Signal sequence recognition protein Ffh
(21)
Thermus aquaticus [TaxId: 271]
(17)
1a
d2j46a1
A:1-88
1b
d2j46b1
B:1-88
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
Nitrogenase iron protein-like
(152)
Protein domain
:
GTPase domain of the signal sequence recognition protein Ffh
(21)
Thermus aquaticus [TaxId: 271]
(17)
2a
d2j46a2
A:89-296
2b
d2j46b2
B:89-297
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2j46A02 (A:91-281)
1b: CATH_2j46B02 (B:91-281)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Thermus aquaticus. Organism_taxid: 271.
(14)
1a
2j46A02
A:91-281
1b
2j46B02
B:91-281
[
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 (457 KB)
Header - Asym.Unit
Biol.Unit 1 (227 KB)
Header - Biol.Unit 1
Biol.Unit 2 (227 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
2J46
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help