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.
2D2O
Asym. Unit
Info
Asym.Unit (220 KB)
Biol.Unit 1 (215 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF A COMPLEX OF THERMOACTINOMYCES VULGARIS R-47 ALPHA-AMYLASE 2 WITH MALTOHEXAOSE DEMONSTRATES THE IMPORTANT ROLE OF AROMATIC RESIDUES AT THE REDUCING END OF THE SUBSTRATE BINDING CLEFT
Authors
:
A. Ohtaki, M. Mizuno, H. Yoshida, T. Tonozuka, Y. Sakano, S. Kamitori
Date
:
13 Sep 05 (Deposition) - 29 Aug 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Beta/Alpha Barrel, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Ohtaki, M. Mizuno, H. Yoshida, T. Tonozuka, Y. Sakano, S. Kamitori
Structure Of A Complex Of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 2 With Maltohexaose Demonstrates The Important Role Of Aromatic Residues At The Reducing End Of The Substrate Binding Cleft
Carbohydr. Res. V. 341 1041 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 14)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: ALPHA-D-GLUCOSE (GLCa)
2b: ALPHA-D-GLUCOSE (GLCb)
2c: ALPHA-D-GLUCOSE (GLCc)
2d: ALPHA-D-GLUCOSE (GLCd)
2e: ALPHA-D-GLUCOSE (GLCe)
2f: ALPHA-D-GLUCOSE (GLCf)
2g: ALPHA-D-GLUCOSE (GLCg)
2h: ALPHA-D-GLUCOSE (GLCh)
2i: ALPHA-D-GLUCOSE (GLCi)
2j: ALPHA-D-GLUCOSE (GLCj)
2k: ALPHA-D-GLUCOSE (GLCk)
2l: ALPHA-D-GLUCOSE (GLCl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
GLC
12
Ligand/Ion
ALPHA-D-GLUCOSE
[
close Hetero Component info
]
Sites
(14, 14)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:164 , ASP A:465 , GLC A:702 , HOH A:1149 , HOH A:1292 , HOH A:1303 , HOH A:1432 , HOH A:1453 , HOH A:1475
BINDING SITE FOR RESIDUE GLC A 701
02
AC2
SOFTWARE
TYR A:204 , HIS A:244 , PHE A:286 , ARG A:323 , ASN A:325 , VAL A:326 , GLU A:354 , HIS A:420 , ASP A:421 , GLC A:702 , GLC A:704
BINDING SITE FOR RESIDUE GLC A 703
03
AC3
SOFTWARE
HIS A:202 , TYR A:204 , MET A:293 , ASP A:465 , ARG A:469 , GLC A:701 , GLC A:703 , HOH A:1149 , HOH A:1234 , HOH A:1374 , HOH A:1475
BINDING SITE FOR RESIDUE GLC A 702
04
AC4
SOFTWARE
PHE A:286 , VAL A:326 , GLU A:354 , TRP A:356 , GLC A:703 , GLC A:705 , HOH A:1005 , HOH A:1050 , HOH A:1475 , TYR B:45
BINDING SITE FOR RESIDUE GLC A 704
05
AC5
SOFTWARE
TRP A:356 , GLC A:704 , GLC A:706 , HOH A:1488 , ARG B:44 , GLN B:112
BINDING SITE FOR RESIDUE GLC A 705
06
AC6
SOFTWARE
TRP A:356 , GLU A:378 , GLC A:705 , HOH A:1245 , HOH A:1370
BINDING SITE FOR RESIDUE GLC A 706
07
AC7
SOFTWARE
HIS B:164 , ASP B:465 , GLC B:702 , HOH B:1159 , HOH B:1167 , HOH B:1204 , HOH B:1278
BINDING SITE FOR RESIDUE GLC B 701
08
AC8
SOFTWARE
TYR B:204 , HIS B:244 , PHE B:286 , ARG B:323 , ASN B:325 , VAL B:326 , GLU B:354 , HIS B:420 , ASP B:421 , GLC B:702 , GLC B:704
BINDING SITE FOR RESIDUE GLC B 703
09
AC9
SOFTWARE
HIS B:202 , TYR B:204 , MET B:293 , ASP B:465 , ARG B:469 , GLC B:701 , GLC B:703 , HOH B:1199 , HOH B:1238 , HOH B:1278
BINDING SITE FOR RESIDUE GLC B 702
10
BC1
SOFTWARE
TYR A:45 , PHE B:286 , VAL B:326 , GLU B:354 , TRP B:356 , GLC B:703 , GLC B:705 , HOH B:1005 , HOH B:1071
BINDING SITE FOR RESIDUE GLC B 704
11
BC2
SOFTWARE
ARG A:44 , GLN A:112 , GLC B:704 , GLC B:706 , HOH B:1006
BINDING SITE FOR RESIDUE GLC B 705
12
BC3
SOFTWARE
GLN A:112 , TRP B:356 , GLU B:378 , GLC B:705
BINDING SITE FOR RESIDUE GLC B 706
13
BC4
SOFTWARE
ASN A:143 , ASP A:145 , ASN A:148 , ASP A:149 , GLY A:169 , ASP A:171 , HOH A:1215
BINDING SITE FOR RESIDUE CA A 1001
14
BC5
SOFTWARE
ASN B:143 , ASP B:145 , ASN B:148 , ASP B:149 , GLY B:169 , ASP B:171 , HOH B:1077
BINDING SITE FOR RESIDUE CA B 1002
[
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, 6)
Info
All SCOP Domains
1a: SCOP_d2d2oa2 (A:503-585)
1b: SCOP_d2d2ob2 (B:503-585)
2a: SCOP_d2d2oa1 (A:1-120)
2b: SCOP_d2d2ob1 (B:1-120)
3a: SCOP_d2d2oa3 (A:121-502)
3b: SCOP_d2d2ob3 (B:121-502)
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
:
Maltogenic amylase
(22)
Thermoactinomyces vulgaris, TVAII [TaxId: 2026]
(11)
1a
d2d2oa2
A:503-585
1b
d2d2ob2
B:503-585
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
E set domains
(509)
Family
:
E-set domains of sugar-utilizing enzymes
(147)
Protein domain
:
Maltogenic amylase, N-terminal domain N
(22)
Thermoactinomyces vulgaris, TVAII [TaxId: 2026]
(11)
2a
d2d2oa1
A:1-120
2b
d2d2ob1
B:1-120
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
:
Maltogenic amylase, central domain
(22)
Thermoactinomyces vulgaris, TVAII [TaxId: 2026]
(11)
3a
d2d2oa3
A:121-502
3b
d2d2ob3
B:121-502
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_2d2oA02 (A:122-242,A:298-502)
1b: CATH_2d2oB02 (B:122-242,B:298-502)
2a: CATH_2d2oA04 (A:503-585)
2b: CATH_2d2oB04 (B:503-585)
3a: CATH_2d2oA01 (A:1-121)
3b: CATH_2d2oB01 (B:1-121)
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)
Thermoactinomyces vulgaris. Organism_taxid: 2026. Strain: r-47.
(23)
1a
2d2oA02
A:122-242,A:298-502
1b
2d2oB02
B:122-242,B:298-502
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Golgi alpha-mannosidase II
(346)
Thermoactinomyces vulgaris. Organism_taxid: 2026. Strain: r-47.
(23)
2a
2d2oA04
A:503-585
2b
2d2oB04
B:503-585
Homologous Superfamily
:
Immunoglobulins
(2282)
Thermoactinomyces vulgaris. Organism_taxid: 2026. Strain: r-47.
(23)
3a
2d2oA01
A:1-121
3b
2d2oB01
B:1-121
[
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
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 (220 KB)
Header - Asym.Unit
Biol.Unit 1 (215 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
2D2O
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help