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.
2PWD
Biol. Unit 1
Info
Asym.Unit (216 KB)
Biol.Unit 1 (108 KB)
Biol.Unit 2 (108 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 THE TREHALULOSE SYNTHASE MUTB FROM PSEUDOMONAS MESOACIDOPHILA MX-45 COMPLEXED TO THE INHIBITOR DEOXYNOJIRMYCIN
Authors
:
S. Ravaud, X. Robert, R. Haser, N. Aghajari
Date
:
11 May 07 (Deposition) - 26 Jun 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Trehalulose Synthase, Sucrose Isomerase, Alpha-Amylase Family, (Beta/Alpha)8 Barrel, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Ravaud, X. Robert, H. Watzlawick, R. Haser, R. Mattes, N. Aghajari
Trehalulose Synthase Native And Carbohydrate Complexed Structures Provide Insights Into Sucrose Isomerization.
J. Biol. Chem. V. 61 100 2007
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: 1-DEOXYNOJIRIMYCIN (NOJa)
2b: 1-DEOXYNOJIRIMYCIN (NOJb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
NOJ
1
Ligand/Ion
1-DEOXYNOJIRIMYCIN
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
ASP A:22 , ASN A:24 , ASP A:26 , ILE A:28 , ASP A:30 , HOH A:4531 , HOH A:4715
BINDING SITE FOR RESIDUE CA A 7001
2
AC3
SOFTWARE
ASP A:61 , TYR A:64 , HIS A:104 , PHE A:145 , PHE A:164 , ARG A:198 , ASP A:200 , GLU A:254 , HIS A:326 , ASP A:327 , ARG A:414 , HOH A:4019 , HOH A:5420
BINDING SITE FOR RESIDUE NOJ A 8000
[
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, 4)
Info
All SCOP Domains
1a: SCOP_d2pwda2 (A:479-557)
1b: SCOP_d2pwdb2 (B:479-557)
2a: SCOP_d2pwda1 (A:1-478)
2b: SCOP_d2pwdb1 (B:1-478)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Glycosyl hydrolase domain
(397)
Superfamily
:
Glycosyl hydrolase domain
(397)
Family
:
automated matches
(85)
Protein domain
:
automated matches
(85)
Pseudomonas mesoacidophila [TaxId: 265293]
(9)
1a
d2pwda2
A:479-557
1b
d2pwdb2
B:479-557
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
Amylase, catalytic domain
(385)
Protein domain
:
automated matches
(71)
Pseudomonas mesoacidophila [TaxId: 265293]
(9)
2a
d2pwda1
A:1-478
2b
d2pwdb1
B:1-478
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_2pwdA01 (A:1-105,A:176-479)
1b: CATH_2pwdB01 (B:1-105,B:176-479)
2a: CATH_2pwdA02 (A:106-175)
2b: CATH_2pwdB02 (B:106-175)
3a: CATH_2pwdA03 (A:480-557)
3b: CATH_2pwdB03 (B:480-557)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
Pseudomonas mesoacidophila. Organism_taxid: 265293. Strain: mx-45.
(5)
1a
2pwdA01
A:1-105,A:176-479
1b
2pwdB01
B:1-105,B:176-479
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Oligo-1,6-glucosidase; domain 2
(22)
Homologous Superfamily
:
Oligo-1,6-glucosidase; Domain 2
(22)
Pseudomonas mesoacidophila. Organism_taxid: 265293. Strain: mx-45.
(5)
2a
2pwdA02
A:106-175
2b
2pwdB02
B:106-175
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Golgi alpha-mannosidase II
(346)
Pseudomonas mesoacidophila. Organism_taxid: 265293. Strain: mx-45.
(5)
3a
2pwdA03
A:480-557
3b
2pwdB03
B:480-557
[
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
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 (216 KB)
Header - Asym.Unit
Biol.Unit 1 (108 KB)
Header - Biol.Unit 1
Biol.Unit 2 (108 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
2PWD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help