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.
2CDO
Biol. Unit 2
Info
Asym.Unit (116 KB)
Biol.Unit 1 (30 KB)
Biol.Unit 2 (30 KB)
Biol.Unit 3 (30 KB)
Biol.Unit 4 (30 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 AGARASE CARBOHYDRATE BINDING MODULE IN COMPLEX WITH NEOAGAROHEXAOSE
Authors
:
J. Henshaw, A. Horne, A. L. Van Bueren, V. A. Money, D. N. Bolam, M. Czjzek, R. M. Weiner, S. W. Hutcheson, G. J. Davies, A. B. Boraston, H. J. Gilbert
Date
:
25 Jan 06 (Deposition) - 16 Feb 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.64
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Carbohydrate-Binding Module, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Henshaw, A. Horne, A. L. Van Bueren, V. A. Money, D. N. Bolam, M. Czjzek, N. A. Ekborg, R. M. Weiner, S. W. Hutcheson, G. J. Davies, A. B. Boraston, H. J. Gilbert
Family 6 Carbohydrate Binding Modules In Beta- Agarases Display Exquisite Selectivity For The Non- Reducing Termini Of Agarose Chains.
J. Biol. Chem. V. 281 17099 2006
[
close entry info
]
Hetero Components
(4, 11)
Info
All Hetero Components
1a: 3,6-ANHYDRO-L-GALACTOSE (AALa)
1b: 3,6-ANHYDRO-L-GALACTOSE (AALb)
1c: 3,6-ANHYDRO-L-GALACTOSE (AALc)
1d: 3,6-ANHYDRO-L-GALACTOSE (AALd)
1e: 3,6-ANHYDRO-L-GALACTOSE (AALe)
1f: 3,6-ANHYDRO-L-GALACTOSE (AALf)
1g: 3,6-ANHYDRO-L-GALACTOSE (AALg)
1h: 3,6-ANHYDRO-L-GALACTOSE (AALh)
1i: 3,6-ANHYDRO-L-GALACTOSE (AALi)
1j: 3,6-ANHYDRO-L-GALACTOSE (AALj)
1k: 3,6-ANHYDRO-L-GALACTOSE (AALk)
1l: 3,6-ANHYDRO-L-GALACTOSE (AALl)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
2g: CALCIUM ION (CAg)
2h: CALCIUM ION (CAh)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
3d: CHLORIDE ION (CLd)
3e: CHLORIDE ION (CLe)
3f: CHLORIDE ION (CLf)
3g: CHLORIDE ION (CLg)
3h: CHLORIDE ION (CLh)
3i: CHLORIDE ION (CLi)
3j: CHLORIDE ION (CLj)
4a: 1,2-ETHANEDIOL (EDOa)
4b: 1,2-ETHANEDIOL (EDOb)
4c: 1,2-ETHANEDIOL (EDOc)
4d: 1,2-ETHANEDIOL (EDOd)
4e: 1,2-ETHANEDIOL (EDOe)
4f: 1,2-ETHANEDIOL (EDOf)
4g: 1,2-ETHANEDIOL (EDOg)
5a: BETA-D-GALACTOSE (GALa)
5b: BETA-D-GALACTOSE (GALb)
5c: BETA-D-GALACTOSE (GALc)
5d: BETA-D-GALACTOSE (GALd)
5e: BETA-D-GALACTOSE (GALe)
5f: BETA-D-GALACTOSE (GALf)
5g: BETA-D-GALACTOSE (GALg)
5h: BETA-D-GALACTOSE (GALh)
5i: BETA-D-GALACTOSE (GALi)
5j: BETA-D-GALACTOSE (GALj)
5k: BETA-D-GALACTOSE (GALk)
5l: BETA-D-GALACTOSE (GALl)
6a: SELENOMETHIONINE (MSEa)
6b: SELENOMETHIONINE (MSEb)
6c: SELENOMETHIONINE (MSEc)
6d: SELENOMETHIONINE (MSEd)
6e: SELENOMETHIONINE (MSEe)
6f: SELENOMETHIONINE (MSEf)
6g: SELENOMETHIONINE (MSEg)
6h: SELENOMETHIONINE (MSEh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AAL
3
Ligand/Ion
3,6-ANHYDRO-L-GALACTOSE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
CL
-1
Ligand/Ion
CHLORIDE ION
4
EDO
3
Ligand/Ion
1,2-ETHANEDIOL
5
GAL
3
Ligand/Ion
BETA-D-GALACTOSE
6
MSE
2
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(18, 18)
Info
All Sites
01: AC7 (SOFTWARE)
02: AC8 (SOFTWARE)
03: AC9 (SOFTWARE)
04: BC1 (SOFTWARE)
05: BC2 (SOFTWARE)
06: BC3 (SOFTWARE)
07: CC5 (SOFTWARE)
08: CC6 (SOFTWARE)
09: CC9 (SOFTWARE)
10: DC3 (SOFTWARE)
11: DC4 (SOFTWARE)
12: DC5 (SOFTWARE)
13: DC6 (SOFTWARE)
14: EC7 (SOFTWARE)
15: EC8 (SOFTWARE)
16: EC9 (SOFTWARE)
17: FC3 (SOFTWARE)
18: FC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC7
SOFTWARE
VAL B:89 , AAL B:1002 , HOH B:2146
BINDING SITE FOR RESIDUE GAL B1001
02
AC8
SOFTWARE
GLU B:75 , SER B:86 , GAL B:1001 , GAL B:1003 , HOH B:2148
BINDING SITE FOR RESIDUE AAL B1002
03
AC9
SOFTWARE
GLU B:75 , MSE B:77 , AAL B:1002 , AAL B:1004 , HOH B:2077 , HOH B:2149 , HOH B:2150
BINDING SITE FOR RESIDUE GAL B1003
04
BC1
SOFTWARE
MSE B:77 , ARG B:118 , HIS B:120 , GAL B:1003 , GAL B:1005 , HOH B:2149
BINDING SITE FOR RESIDUE AAL B1004
05
BC2
SOFTWARE
TYR B:46 , ARG B:118 , AAL B:1004 , AAL B:1006 , HOH B:2020 , HOH B:2057 , HOH B:2151 , VAL D:69 , TRP D:97 , HOH D:2125
BINDING SITE FOR RESIDUE GAL B1005
06
BC3
SOFTWARE
GLY B:16 , TYR B:46 , GAL B:1005 , HOH B:2020 , HOH B:2152 , HOH B:2153 , ASN D:39 , TYR D:40 , TRP D:97 , TRP D:127 , ASN D:130
BINDING SITE FOR RESIDUE AAL B1006
07
CC5
SOFTWARE
TRP B:97 , TYR D:46 , ARG D:118 , AAL D:1004 , AAL D:1006 , HOH D:2049 , HOH D:2143 , HOH D:2144 , HOH D:2145
BINDING SITE FOR RESIDUE GAL D1005
08
CC6
SOFTWARE
ASN B:39 , TYR B:40 , TRP B:97 , TRP B:127 , ASN B:130 , HOH B:2106 , TYR D:46 , GAL D:1005 , HOH D:2146
BINDING SITE FOR RESIDUE AAL D1006
09
CC9
SOFTWARE
GLU A:8 , ASN A:11 , ASN B:104
BINDING SITE FOR RESIDUE CL A1141
10
DC3
SOFTWARE
GLU B:8 , GLU B:10 , THR B:36 , ASP B:132 , HOH B:2046
BINDING SITE FOR RESIDUE CA B1139
11
DC4
SOFTWARE
ASP B:21 , PRO B:26 , TYR B:40 , ASN B:42 , ASP B:45 , HOH B:2021
BINDING SITE FOR RESIDUE CA B1140
12
DC5
SOFTWARE
GLU B:8 , ASN B:11 , HOH B:2003
BINDING SITE FOR RESIDUE CL B1143
13
DC6
SOFTWARE
TYR B:109 , HOH B:2118 , HOH B:2120
BINDING SITE FOR RESIDUE CL B1144
14
EC7
SOFTWARE
VAL A:53 , ALA A:54 , VAL B:69 , THR B:70 , GLY B:71 , VAL B:92 , HOH B:2096 , HOH B:2154 , HOH B:2155 , HOH B:2156
BINDING SITE FOR RESIDUE EDO B1141
15
EC8
SOFTWARE
THR A:70 , PRO A:93 , ASN A:94 , HOH A:2094 , GLY B:57 , ASN B:58 , TYR B:109 , HOH B:2157
BINDING SITE FOR RESIDUE EDO B1142
16
EC9
SOFTWARE
GLY B:96 , TRP B:97 , ASP B:98 , HOH B:2158 , HOH D:2051
BINDING SITE FOR RESIDUE EDO B1145
17
FC3
SOFTWARE
ASN B:81 , LYS C:87 , VAL C:108 , TYR C:109 , HOH C:2138 , HOH C:2139
BINDING SITE FOR RESIDUE EDO C1146
18
FC4
SOFTWARE
ALA B:52 , VAL B:53 , ALA B:54 , HOH B:2125 , HOH D:2147
BINDING SITE FOR RESIDUE EDO D1143
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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 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 (116 KB)
Header - Asym.Unit
Biol.Unit 1 (30 KB)
Header - Biol.Unit 1
Biol.Unit 2 (30 KB)
Header - Biol.Unit 2
Biol.Unit 3 (30 KB)
Header - Biol.Unit 3
Biol.Unit 4 (30 KB)
Header - Biol.Unit 4
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
2CDO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
