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.
3RE3
Biol. Unit 3
Info
Asym.Unit (211 KB)
Biol.Unit 1 (158 KB)
Biol.Unit 2 (151 KB)
Biol.Unit 3 (600 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE FROM FRANCISELLA TULARENSIS
Authors
:
Y. Kim, M. Makowska-Grzyska, K. Kwon, W. F. Anderson, A. Joachimiak, Ce Structural Genomics Of Infectious Diseases (Csgid)
Date
:
02 Apr 11 (Deposition) - 27 Apr 11 (Release) - 27 Apr 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.65
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (3x)
Biol. Unit 2: B,C,D (1x)
Biol. Unit 3: A,B,C,D (3x)
Keywords
:
Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Alpha-Beta Half Sandwich, Cytosol, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Kim, M. Makowska-Grzyska, K. Kwon, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of 2-C-Methyl-D-Erythritol 2, 4-Cyclodiphosphate Synthase From Francisella Tularensis
To Be Published
[
close entry info
]
Hetero Components
(4, 69)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
2b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
5a: PHOSPHATE ION (PO4a)
5b: PHOSPHATE ION (PO4b)
5c: PHOSPHATE ION (PO4c)
6a: PYROPHOSPHATE 2- (POPa)
6b: PYROPHOSPHATE 2- (POPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
MPD
6
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
MSE
48
Mod. Amino Acid
SELENOMETHIONINE
4
NA
-1
Ligand/Ion
SODIUM ION
5
PO4
9
Ligand/Ion
PHOSPHATE ION
6
POP
6
Ligand/Ion
PYROPHOSPHATE 2-
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:10 , VAL A:11 , HIS A:12 , GLY A:40 , VAL A:42 , HIS A:45 , GLU A:138
BINDING SITE FOR RESIDUE POP A 163
02
AC2
SOFTWARE
ARG A:4 , GLY A:53 , ALA A:54 , ASN A:96 , ILE A:97 , ASN A:131
BINDING SITE FOR RESIDUE NA A 165
03
AC3
SOFTWARE
GLY A:141 , ARG A:145 , PO4 A:161
BINDING SITE FOR RESIDUE CL A 160
04
AC4
SOFTWARE
GLY A:141 , PHE A:142 , CL A:160 , HOH A:187
BINDING SITE FOR RESIDUE PO4 A 161
05
AC5
SOFTWARE
ASP B:10 , VAL B:11 , HIS B:12 , ASP B:39 , GLY B:40 , VAL B:42 , HIS B:45 , HOH B:165 , THR C:136 , GLU C:138 , HOH C:171
BINDING SITE FOR RESIDUE POP B 161
06
AC6
SOFTWARE
ASN B:96 , ILE B:97 , ASN B:131 , ARG D:4 , GLY D:53
BINDING SITE FOR RESIDUE NA B 160
07
AC7
SOFTWARE
HIS B:152 , HIS C:152 , HOH C:170 , HIS D:152
BINDING SITE FOR RESIDUE PO4 C 162
08
AC8
SOFTWARE
GLY B:141 , PHE B:142 , GLY C:141 , PHE C:142 , HOH C:169 , PHE D:142 , PO4 D:162
BINDING SITE FOR RESIDUE MPD C 163
09
AC9
SOFTWARE
ARG C:4 , GLY C:53 , ALA C:54 , ASN D:96 , ILE D:97 , ASN D:131
BINDING SITE FOR RESIDUE NA C 161
10
BC1
SOFTWARE
ASP C:10 , VAL C:11 , HIS C:45 , HOH C:166 , THR D:135 , THR D:136 , GLU D:138
BINDING SITE FOR RESIDUE MPD C 160
11
BC2
SOFTWARE
GLY B:141 , ARG B:145 , GLY C:141 , ARG C:145 , MPD C:163 , GLY D:141 , PHE D:142 , ARG D:145
BINDING SITE FOR RESIDUE PO4 D 162
12
BC3
SOFTWARE
ASP D:10
BINDING SITE FOR RESIDUE CL D 160
[
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
(1, 12)
Info
All PROSITE Patterns/Profiles
1: ISPF (A:39-53,B:39-53,C:39-53,D:40-53)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ISPF
PS01350
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.
ISPF_FRATT
38-53
12
A:39-53
B:39-53
C:39-53
D:40-53
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3re3a_ (A:)
1b: SCOP_d3re3b_ (B:)
1c: SCOP_d3re3c_ (C:)
1d: SCOP_d3re3d_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Bacillus chorismate mutase-like
(324)
Superfamily
:
IpsF-like
(56)
Family
:
automated matches
(21)
Protein domain
:
automated matches
(21)
Francisella tularensis [TaxId: 177416]
(1)
1a
d3re3a_
A:
1b
d3re3b_
B:
1c
d3re3c_
C:
1d
d3re3d_
D:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_YgbB_3re3D01 (D:3-159)
1b: PFAM_YgbB_3re3D02 (D:3-159)
1c: PFAM_YgbB_3re3D03 (D:3-159)
1d: PFAM_YgbB_3re3D04 (D:3-159)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: YgbB]
(24)
Family
:
YgbB
(24)
Francisella tularensis subsp. tularensis
(1)
1a
YgbB-3re3D01
D:3-159
1b
YgbB-3re3D02
D:3-159
1c
YgbB-3re3D03
D:3-159
1d
YgbB-3re3D04
D:3-159
[
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
Asymmetric Unit 2
Asymmetric Unit 3
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 (211 KB)
Header - Asym.Unit
Biol.Unit 1 (158 KB)
Header - Biol.Unit 1
Biol.Unit 2 (151 KB)
Header - Biol.Unit 2
Biol.Unit 3 (600 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
3RE3
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help