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.
1UKQ
Biol. Unit 1
Info
Asym.Unit (236 KB)
Biol.Unit 1 (119 KB)
Biol.Unit 2 (117 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 CYCLODEXTRIN GLUCANOTRANSFERASE COMPLEXED WITH A PSEUDO-MALTOTETRAOSE DERIVED FROM ACARBOSE
Authors
:
K. Haga, R. Kanai, O. Sakamoto, K. Harata, K. Yamane
Date
:
01 Sep 03 (Deposition) - 24 Feb 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Cgtase, Acarbose, Carbohydrate-Protein Complex, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Haga, R. Kanai, O. Sakamoto, M. Aoyagi, K. Harata, K. Yamane
Effects Of Essential Carbohydrate/Aromatic Stacking Interaction With Tyr100 And Phe259 On Substrate Binding Of Cyclodextrin Glycosyltransferase From Alkalophilic Bacillus Sp. 1011
J. Biochem. (Tokyo) V. 134 881 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 4)
Info
All Hetero Components
1a: 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4... (ACIa)
1b: 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4... (ACIb)
2a: BETA-D-GLUCOSE (BGCa)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
3c: CALCIUM ION (CAc)
3d: CALCIUM ION (CAd)
4a: 6-DEOXY-ALPHA-D-GLUCOSE (G6Da)
4b: 6-DEOXY-ALPHA-D-GLUCOSE (G6Db)
5a: ALPHA-D-GLUCOSE (GLCa)
5b: ALPHA-D-GLUCOSE (GLCb)
5c: ALPHA-D-GLUCOSE (GLCc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACI
1
Ligand/Ion
6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
2
BGC
1
Ligand/Ion
BETA-D-GLUCOSE
3
CA
-1
Ligand/Ion
CALCIUM ION
4
G6D
1
Ligand/Ion
6-DEOXY-ALPHA-D-GLUCOSE
5
GLC
1
Ligand/Ion
ALPHA-D-GLUCOSE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC9 (SOFTWARE)
6: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:100 , TRP A:101 , ASP A:371 , ARG A:375 , ACI A:702 , HOH A:1429 , HOH A:1480
BINDING SITE FOR RESIDUE GLC A 701
2
AC2
SOFTWARE
TYR A:100 , HIS A:140 , LEU A:197 , ASP A:229 , GLU A:257 , HIS A:327 , ASP A:328 , ARG A:375 , GLC A:701 , G6D A:703 , HOH A:1529
BINDING SITE FOR RESIDUE ACI A 702
3
AC3
SOFTWARE
LEU A:194 , TYR A:195 , HIS A:233 , GLU A:257 , PHE A:259 , ACI A:702 , BGC A:704 , HOH A:1477
BINDING SITE FOR RESIDUE G6D A 703
4
AC4
SOFTWARE
ASP A:328 , G6D A:703
BINDING SITE FOR RESIDUE BGC A 704
5
AC9
SOFTWARE
ASP A:27 , ASN A:29 , ASN A:32 , ASN A:33 , GLY A:51 , ASP A:53 , HOH A:1444
BINDING SITE FOR RESIDUE CA A 687
6
BC1
SOFTWARE
ASN A:139 , ILE A:190 , ASP A:199 , HIS A:233 , HOH A:1289 , HOH A:1456 , HOH A:1599
BINDING SITE FOR RESIDUE CA A 688
[
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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: CBM20 (A:581-686)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CBM20
PS51166
CBM20 (carbohydrate binding type-20) domain profile.
CDGT_BACS0
608-713
1
A:581-686
-
[
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, 8)
Info
All SCOP Domains
1a: SCOP_d1ukqa3 (A:407-495)
1b: SCOP_d1ukqb3 (B:407-495)
2a: SCOP_d1ukqa1 (A:496-581)
2b: SCOP_d1ukqb1 (B:496-581)
3a: SCOP_d1ukqa2 (A:582-686)
3b: SCOP_d1ukqb2 (B:582-686)
4a: SCOP_d1ukqa4 (A:1-406)
4b: SCOP_d1ukqb4 (B:1-406)
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
:
Cyclodextrin glycosyltransferase
(51)
Bacillus circulans, different strains [TaxId: 1397]
(36)
1a
d1ukqa3
A:407-495
1b
d1ukqb3
B:407-495
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
E set domains
(509)
Family
:
E-set domains of sugar-utilizing enzymes
(147)
Protein domain
:
Cyclomaltodextrin glycanotransferase, domain D
(49)
Bacillus circulans, different strains [TaxId: 1397]
(36)
2a
d1ukqa1
A:496-581
2b
d1ukqb1
B:496-581
Fold
:
Prealbumin-like
(433)
Superfamily
:
Starch-binding domain-like
(84)
Family
:
Starch-binding domain
(67)
Protein domain
:
Cyclodextrin glycosyltransferase, C-terminal domain
(51)
Bacillus circulans, different strains [TaxId: 1397]
(36)
3a
d1ukqa2
A:582-686
3b
d1ukqb2
B:582-686
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
:
Cyclodextrin glycosyltransferase
(51)
Bacillus circulans, different strains [TaxId: 1397]
(36)
4a
d1ukqa4
A:1-406
4b
d1ukqb4
B:1-406
[
close SCOP info
]
CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_1ukqA01 (A:1-400)
1b: CATH_1ukqB01 (B:1-400)
2a: CATH_1ukqA02 (A:401-495)
2b: CATH_1ukqB02 (B:401-495)
3a: CATH_1ukqA04 (A:583-685)
3b: CATH_1ukqA03 (A:496-582)
3c: CATH_1ukqB03 (B:496-582)
3d: CATH_1ukqB04 (B:583-685)
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)
1011 (Bacillus sp)
(10)
1a
1ukqA01
A:1-400
1b
1ukqB01
B:1-400
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Golgi alpha-mannosidase II
(346)
1011 (Bacillus sp)
(10)
2a
1ukqA02
A:401-495
2b
1ukqB02
B:401-495
Homologous Superfamily
:
Immunoglobulins
(2282)
1011 (Bacillus sp)
(10)
3a
1ukqA04
A:583-685
3b
1ukqA03
A:496-582
3c
1ukqB03
B:496-582
3d
1ukqB04
B:583-685
[
close CATH info
]
Pfam Domains
(4, 8)
Info
all PFAM domains
1a: PFAM_TIG_1ukqB01 (B:499-581)
1b: PFAM_TIG_1ukqB02 (B:499-581)
2a: PFAM_Alpha_amylase_C_1ukqB03 (B:413-494)
2b: PFAM_Alpha_amylase_C_1ukqB04 (B:413-494)
3a: PFAM_CBM_20_1ukqB05 (B:586-682)
3b: PFAM_CBM_20_1ukqB06 (B:586-682)
4a: PFAM_Alpha_amylase_1ukqB07 (B:52-372)
4b: PFAM_Alpha_amylase_1ukqB08 (B:52-372)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
E-set
(290)
Family
:
TIG
(28)
Bacillus sp. (strain 1011)
(8)
1a
TIG-1ukqB01
B:499-581
1b
TIG-1ukqB02
B:499-581
Clan
:
GHD
(106)
Family
:
Alpha-amylase_C
(82)
Bacillus sp. (strain 1011)
(8)
2a
Alpha-amylase_C-1ukqB03
B:413-494
2b
Alpha-amylase_C-1ukqB04
B:413-494
Family
:
CBM_20
(20)
Bacillus sp. (strain 1011)
(8)
3a
CBM_20-1ukqB05
B:586-682
3b
CBM_20-1ukqB06
B:586-682
Clan
:
Glyco_hydro_tim
(488)
Family
:
Alpha-amylase
(138)
Bacillus sp. (strain 1011)
(8)
4a
Alpha-amylase-1ukqB07
B:52-372
4b
Alpha-amylase-1ukqB08
B:52-372
[
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 (236 KB)
Header - Asym.Unit
Biol.Unit 1 (119 KB)
Header - Biol.Unit 1
Biol.Unit 2 (117 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
1UKQ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
