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.
3A9S
Biol. Unit 1
Info
Asym.Unit (314 KB)
Biol.Unit 1 (610 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY STRUCTURE OF BACILLUS PALLIDUS D-ARABINOSE ISOMERASE COMPLEX WITH GLYCEROL
Authors
:
K. Takeda, H. Yoshida, K. Izumori, S. Kamitori
Date
:
05 Nov 09 (Deposition) - 07 Apr 10 (Release) - 07 Apr 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (2x)
Keywords
:
Rossmann Fold, Beta Barrel, Carbohydrate Metabolism, Cytoplasm, Fucose Metabolism, Isomerase, Manganese, Metal- Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Takeda, H. Yoshida, K. Izumori, S. Kamitori
X-Ray Structures Of Bacillus Pallidusd-Arabinose Isomerase And Its Complex With L-Fucitol.
Biochim. Biophys. Acta V. 1804 1359 2010
[
close entry info
]
Hetero Components
(1, 12)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
2e: MANGANESE (II) ION (MNe)
2f: MANGANESE (II) ION (MNf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
12
Ligand/Ion
GLYCEROL
2
MN
-1
Ligand/Ion
MANGANESE (II) ION
[
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
GLN A:307 , GLU A:342 , ASP A:366 , SER A:398 , MN A:701 , HOH A:702 , ARG B:23 , TRP B:95
BINDING SITE FOR RESIDUE GOL A 601
02
AC2
SOFTWARE
GLU A:342 , ASP A:366 , ASN A:397 , SER A:398 , HIS A:532 , GOL A:601 , HOH A:702
BINDING SITE FOR RESIDUE MN A 701
03
AC3
SOFTWARE
ASP A:453 , HOH A:802 , HOH A:803 , HOH A:804 , HOH A:805 , HOH A:806
BINDING SITE FOR RESIDUE MN A 801
04
AC4
SOFTWARE
ASN A:49 , VAL A:50 , PHE A:51 , LYS A:169 , LEU A:357 , THR A:358 , ASN A:359 , HOH A:848 , HOH A:961
BINDING SITE FOR RESIDUE GOL A 901
05
AC5
SOFTWARE
MET B:190 , GLN B:307 , GLU B:342 , ASP B:366 , SER B:398 , MN B:701 , HOH B:702 , ARG C:23 , TRP C:95
BINDING SITE FOR RESIDUE GOL B 601
06
AC6
SOFTWARE
GLU B:342 , ASP B:366 , ASN B:397 , SER B:398 , HIS B:532 , GOL B:601 , HOH B:702
BINDING SITE FOR RESIDUE MN B 701
07
AC7
SOFTWARE
ASP B:453 , HOH B:802 , HOH B:803 , HOH B:804 , HOH B:805 , HOH B:806
BINDING SITE FOR RESIDUE MN B 801
08
AC8
SOFTWARE
ASN B:49 , VAL B:50 , PHE B:51 , LYS B:169 , LEU B:357 , THR B:358 , ASN B:359 , HOH B:793 , HOH B:908
BINDING SITE FOR RESIDUE GOL B 901
09
AC9
SOFTWARE
GLU C:342 , ASP C:366 , ASN C:397 , SER C:398 , HIS C:532 , GOL C:601 , HOH C:702
BINDING SITE FOR RESIDUE MN C 701
10
BC1
SOFTWARE
ARG A:23 , TRP A:95 , MET C:190 , GLN C:307 , GLU C:342 , ASP C:366 , SER C:398 , MN C:701 , HOH C:702
BINDING SITE FOR RESIDUE GOL C 601
11
BC2
SOFTWARE
ASP C:453 , HOH C:802 , HOH C:803 , HOH C:804 , HOH C:805 , HOH C:806
BINDING SITE FOR RESIDUE MN C 801
12
BC3
SOFTWARE
ASN C:49 , VAL C:50 , PHE C:51 , LYS C:169 , LEU C:357 , THR C:358 , ASN C:359 , HOH C:783 , HOH C:952
BINDING SITE FOR RESIDUE GOL C 901
[
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
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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
(2, 6)
Info
All SCOP Domains
1a: SCOP_d3a9sa2 (A:361-590)
1b: SCOP_d3a9sb2 (B:361-590)
1c: SCOP_d3a9sc2 (C:361-590)
2a: SCOP_d3a9sa1 (A:2-360)
2b: SCOP_d3a9sb1 (B:2-360)
2c: SCOP_d3a9sc1 (C:2-360)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Reductase/isomerase/elongation factor common domain
(381)
Superfamily
:
FucI/AraA C-terminal domain-like
(10)
Family
:
automated matches
(7)
Protein domain
:
automated matches
(7)
Geobacillus pallidus [TaxId: 33936]
(3)
1a
d3a9sa2
A:361-590
1b
d3a9sb2
B:361-590
1c
d3a9sc2
C:361-590
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
FucI/AraA N-terminal and middle domains
(10)
Superfamily
:
FucI/AraA N-terminal and middle domains
(10)
Family
:
automated matches
(6)
Protein domain
:
automated matches
(6)
Geobacillus pallidus [TaxId: 33936]
(3)
2a
d3a9sa1
A:2-360
2b
d3a9sb1
B:2-360
2c
d3a9sc1
C:2-360
[
close SCOP info
]
CATH Domains
(3, 9)
Info
all CATH domains
1a: CATH_3a9sA02 (A:181-345)
1b: CATH_3a9sB02 (B:181-345)
1c: CATH_3a9sC02 (C:181-345)
2a: CATH_3a9sA01 (A:2-180)
2b: CATH_3a9sB01 (B:2-180)
2c: CATH_3a9sC01 (C:2-180)
3a: CATH_3a9sA03 (A:346-590)
3b: CATH_3a9sB03 (B:346-590)
3c: CATH_3a9sC03 (C:346-590)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
L-fucose Isomerase; Chain A, domain 2
(4)
Homologous Superfamily
:
L-fucose Isomerase; Chain A, domain 2
(4)
Geobacillus pallidus. Organism_taxid: 33936. Strain: 14a.
(3)
1a
3a9sA02
A:181-345
1b
3a9sB02
B:181-345
1c
3a9sC02
C:181-345
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1070, no name defined]
(4)
Geobacillus pallidus. Organism_taxid: 33936. Strain: 14a.
(3)
2a
3a9sA01
A:2-180
2b
3a9sB01
B:2-180
2c
3a9sC01
C:2-180
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
L-fucose Isomerase; Chain A, domain 3
(4)
Homologous Superfamily
:
L-fucose Isomerase; Chain A, domain 3
(4)
Geobacillus pallidus. Organism_taxid: 33936. Strain: 14a.
(3)
3a
3a9sA03
A:346-590
3b
3a9sB03
B:346-590
3c
3a9sC03
C:346-590
[
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
Chain C
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 (314 KB)
Header - Asym.Unit
Biol.Unit 1 (610 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
3A9S
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help