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.
3VGE
Asym. Unit
Info
Asym.Unit (197 KB)
Biol.Unit 1 (191 KB)
Biol.Unit 2 (380 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 GLYCOSYLTREHALOSE TREHALOHYDROLASE (D252S)
Authors
:
N. Okazaki, T. Tamada, M. D. Feese, M. Kato, Y. Miura, T. Komeda, K. Kobay K. Kondo, R. Kuroki
Date
:
09 Aug 11 (Deposition) - 20 Jun 12 (Release) - 20 Jun 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Biol. Unit 2: A (2x)
Keywords
:
Alpha/Beta Barrel, Trehalose, Trehalohydrolase, Alpha-Amylase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Okazaki, T. Tamada, M. D. Feese, M. Kato, Y. Miura, T. Komeda, K. Kobayashi, K. Kondo, M. Blaber, R. Kuroki
Substrate Recognition Mechanism Of A Glycosyltrehalose Trehalohydrolase From Sulfolobus Solfataricus Km1.
Protein Sci. V. 21 539 2012
[
close entry info
]
Hetero Components
(2, 8)
Info
All Hetero Components
1a: CITRATE ANION (FLCa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FLC
1
Ligand/Ion
CITRATE ANION
2
GOL
7
Ligand/Ion
GLYCEROL
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:323 , ARG A:382 , GLY A:383 , LYS A:384 , ASN A:448 , GOL A:1104 , HOH A:2094 , HOH A:2095
BINDING SITE FOR RESIDUE FLC A 1001
2
AC2
SOFTWARE
GLU A:115 , GLY A:116 , SER A:163 , PHE A:460
BINDING SITE FOR RESIDUE GOL A 1101
3
AC3
SOFTWARE
ARG A:123 , LYS A:124 , TRP A:467 , SER A:537 , GLU A:548 , HOH A:2009
BINDING SITE FOR RESIDUE GOL A 1102
4
AC4
SOFTWARE
LYS A:99 , VAL A:292 , ILE A:302 , ASP A:303 , ASN A:368 , HOH A:2145 , HOH A:2146
BINDING SITE FOR RESIDUE GOL A 1103
5
AC5
SOFTWARE
GLN A:323 , TYR A:325 , ARG A:382 , FLC A:1001 , HOH A:2046 , HOH A:2057
BINDING SITE FOR RESIDUE GOL A 1104
6
AC6
SOFTWARE
TYR A:127 , LYS A:519 , GLU A:548 , HOH A:2020
BINDING SITE FOR RESIDUE GOL A 1105
7
AC7
SOFTWARE
ILE A:85 , SER A:88 , ARG A:171 , GLU A:243
BINDING SITE FOR RESIDUE GOL A 1106
8
AC8
SOFTWARE
TRP A:215 , ARG A:250 , SER A:252 , GLU A:283 , HIS A:376 , ASP A:377
BINDING SITE FOR RESIDUE GOL A 1107
[
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
(0, 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.
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d3vgea3 (A:491-557)
2a: SCOP_d3vgea1 (A:3-90)
3a: SCOP_d3vgea2 (A:91-490)
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
:
alpha-Amylases, C-terminal beta-sheet domain
(272)
Protein domain
:
Glycosyltrehalose trehalohydrolase
(17)
Sulfolobus solfataricus, km1 [TaxId: 2287]
(8)
1a
d3vgea3
A:491-557
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
E set domains
(509)
Family
:
E-set domains of sugar-utilizing enzymes
(147)
Protein domain
:
Glycosyltrehalose trehalohydrolase, N-terminal domain N
(17)
Sulfolobus solfataricus, km1 [TaxId: 2287]
(8)
2a
d3vgea1
A:3-90
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
:
Glycosyltrehalose trehalohydrolase, central domain
(17)
Sulfolobus solfataricus, km1 [TaxId: 2287]
(8)
3a
d3vgea2
A:91-490
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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 (197 KB)
Header - Asym.Unit
Biol.Unit 1 (191 KB)
Header - Biol.Unit 1
Biol.Unit 2 (380 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
3VGE
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
