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.
1UG9
Biol. Unit 1
Info
Asym.Unit (168 KB)
Biol.Unit 1 (163 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 GLUCODEXTRANASE FROM ARTHROBACTER GLOBIFORMIS I42
Authors
:
M. Mizuno, T. Tonozuka, S. Suzuki, R. Uotsu-Tomita, A. Ohtaki, S. Kamit A. Nishikawa, Y. Sakano
Date
:
16 Jun 03 (Deposition) - 09 Dec 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Alpha-Alpha-Six-Barrels, Gh Family 15, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Mizuno, T. Tonozuka, S. Suzuki, R. Uotsu-Tomita, S. Kamitori, A. Nishikawa, Y. Sakano
Structural Insights Into Substrate Specificity And Function Of Glucodextranase
J. Biol. Chem. V. 279 10575 2004
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
2a: GLYCEROL (GOLa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
GOL
1
Ligand/Ion
GLYCEROL
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU A:139 , THR A:142 , GLY A:144 , ASP A:146 , ASP A:159
BINDING SITE FOR RESIDUE CA A 2001
2
AC2
SOFTWARE
PHE A:358 , GLN A:362 , GLU A:409 , HOH A:3404
BINDING SITE FOR RESIDUE CA A 2002
3
AC3
SOFTWARE
ASP A:136 , PRO A:137 , ASN A:211 , ILE A:212 , HOH A:3061
BINDING SITE FOR RESIDUE CA A 2003
4
AC4
SOFTWARE
VAL A:946 , ALA A:969 , ASP A:980 , ASP A:982 , ASP A:985
BINDING SITE FOR RESIDUE CA A 2004
5
AC5
SOFTWARE
ASP A:782 , PRO A:783 , ASP A:786 , ASP A:807 , LEU A:808 , ASP A:990
BINDING SITE FOR RESIDUE CA A 2005
6
AC6
SOFTWARE
ASP A:782 , ASP A:786 , ASP A:990 , VAL A:991 , GLN A:999 , HOH A:3199
BINDING SITE FOR RESIDUE CA A 2006
7
AC7
SOFTWARE
GLY A:526 , LEU A:529 , TRP A:565 , LEU A:594 , GLU A:597 , ARG A:598 , HOH A:3163
BINDING SITE FOR RESIDUE GOL A 3001
[
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
(4, 4)
Info
All SCOP Domains
1a: SCOP_d1ug9a1 (A:274-686)
2a: SCOP_d1ug9a3 (A:776-1020)
3a: SCOP_d1ug9a2 (A:687-775)
4a: SCOP_d1ug9a4 (A:2-273)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
alpha/alpha toroid
(324)
Superfamily
:
Six-hairpin glycosidases
(109)
Family
:
Bacterial glucoamylase C-terminal domain-like
(4)
Protein domain
:
Glucodextranase, domain A
(2)
Arthrobacter globiformis [TaxId: 1665]
(2)
1a
d1ug9a1
A:274-686
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
CBD9-like
(9)
Family
:
Glucodextranase, domain C
(2)
Protein domain
:
Glucodextranase, domain C
(2)
Arthrobacter globiformis [TaxId: 1665]
(2)
2a
d1ug9a3
A:776-1020
Superfamily
:
E set domains
(509)
Family
:
E-set domains of sugar-utilizing enzymes
(147)
Protein domain
:
Glucodextranase, domain B
(2)
Arthrobacter globiformis [TaxId: 1665]
(2)
3a
d1ug9a2
A:687-775
Fold
:
Supersandwich
(271)
Superfamily
:
Galactose mutarotase-like
(205)
Family
:
Bacterial glucoamylase N-terminal domain-like
(4)
Protein domain
:
Glucodextranase, domain N
(2)
Arthrobacter globiformis [TaxId: 1665]
(2)
4a
d1ug9a4
A:2-273
[
close SCOP info
]
CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_1ug9A02 (A:274-687)
2a: CATH_1ug9A01 (A:2-273)
3a: CATH_1ug9A04 (A:774-938,A:939-1020)
4a: CATH_1ug9A03 (A:688-773)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Alpha/alpha barrel
(251)
Topology
:
Glycosyltransferase
(233)
Homologous Superfamily
:
[code=1.50.10.10, no name defined]
(67)
Arthrobacter globiformis. Organism_taxid: 1665. Strain: i42
(2)
1a
1ug9A02
A:274-687
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Beta-galactosidase; Chain A, domain 5
(250)
Homologous Superfamily
:
[code=2.70.98.10, no name defined]
(116)
Arthrobacter globiformis. Organism_taxid: 1665. Strain: i42
(2)
2a
1ug9A01
A:2-273
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.1190, no name defined]
(5)
Arthrobacter globiformis. Organism_taxid: 1665. Strain: i42
(2)
3a
1ug9A04
A:774-938,A:939-1020
Homologous Superfamily
:
E-set domains of sugar-utilizing enzymes; domain 3
(3)
Arthrobacter globiformis. Organism_taxid: 1665. Strain: i42
(2)
4a
1ug9A03
A:688-773
[
close CATH info
]
Pfam Domains
(4, 4)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_15_1ug9A01 (A:281-956)
2a: PFAM_DUF2223_1ug9A02 (A:776-1018)
3a: PFAM_Glucodextran_B_1ug9A03 (A:692-775)
4a: PFAM_Glucodextran_N_1ug9A04 (A:5-271)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
6_Hairpin
(120)
Family
:
Glyco_hydro_15
(4)
Arthrobacter globiformis
(2)
1a
Glyco_hydro_15-1ug9A01
A:281-956
Clan
:
no clan defined [family: DUF2223]
(2)
Family
:
DUF2223
(2)
Arthrobacter globiformis
(2)
2a
DUF2223-1ug9A02
A:776-1018
Clan
:
no clan defined [family: Glucodextran_B]
(2)
Family
:
Glucodextran_B
(2)
Arthrobacter globiformis
(2)
3a
Glucodextran_B-1ug9A03
A:692-775
Clan
:
no clan defined [family: Glucodextran_N]
(4)
Family
:
Glucodextran_N
(4)
Arthrobacter globiformis
(2)
4a
Glucodextran_N-1ug9A04
A:5-271
[
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 (168 KB)
Header - Asym.Unit
Biol.Unit 1 (163 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
1UG9
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
