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.
2YFO
Asym. Unit
Info
Asym.Unit (267 KB)
Biol.Unit 1 (1022 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
GALACTOSIDASE DOMAIN OF ALPHA-GALACTOSIDASE-SUCROSE KINASE, AGASK, IN COMPLEX WITH GALACTOSE
Authors
:
G. Sulzenbacher, L. Bruel, M. Tison-Cervera, A. Pujol, C. Nicoletti, J A. Galinier, D. Ropartz, M. Fons, F. Pompeo, T. Giardina
Date
:
07 Apr 11 (Deposition) - 28 Sep 11 (Release) - 07 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.35
Chains
:
Asym. Unit : A
Biol. Unit 1: A (4x)
Keywords
:
Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Bruel, G. Sulzenbacher, M. Tison-Cervera, A. Pujol, C. Nicoletti, J. Perrier, A. Galinier, D. Ropartz, M. Fons, F. Pompeo, T. Giardina
Agask, A Bifunctional Enzyme From The Human Microbiome Coupling Galactosidase And Kinase Activities
J. Biol. Chem. V. 286 40814 2011
[
close entry info
]
Hetero Components
(6, 35)
Info
All Hetero Components
1a: BETA-D-GALACTOSE (GALa)
2a: ALPHA D-GALACTOSE (GLAa)
3a: GLYCEROL (GOLa)
4a: SODIUM ION (NAa)
4aa: SODIUM ION (NAaa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
4e: SODIUM ION (NAe)
4f: SODIUM ION (NAf)
4g: SODIUM ION (NAg)
4h: SODIUM ION (NAh)
4i: SODIUM ION (NAi)
4j: SODIUM ION (NAj)
4k: SODIUM ION (NAk)
4l: SODIUM ION (NAl)
4m: SODIUM ION (NAm)
4n: SODIUM ION (NAn)
4o: SODIUM ION (NAo)
4p: SODIUM ION (NAp)
4q: SODIUM ION (NAq)
4r: SODIUM ION (NAr)
4s: SODIUM ION (NAs)
4t: SODIUM ION (NAt)
4u: SODIUM ION (NAu)
4v: SODIUM ION (NAv)
4w: SODIUM ION (NAw)
4x: SODIUM ION (NAx)
4y: SODIUM ION (NAy)
4z: SODIUM ION (NAz)
5a: TRIETHYLENE GLYCOL (PGEa)
5b: TRIETHYLENE GLYCOL (PGEb)
5c: TRIETHYLENE GLYCOL (PGEc)
5d: TRIETHYLENE GLYCOL (PGEd)
6a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GAL
1
Ligand/Ion
BETA-D-GALACTOSE
2
GLA
1
Ligand/Ion
ALPHA D-GALACTOSE
3
GOL
1
Ligand/Ion
GLYCEROL
4
NA
27
Ligand/Ion
SODIUM ION
5
PGE
4
Ligand/Ion
TRIETHYLENE GLYCOL
6
PO4
1
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(35, 35)
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)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:81 , THR A:82 , GLY A:83 , ASP A:84 , TYR A:85 , ARG A:220 , ALA A:484 , ASP A:485 , VAL A:486 , HOH A:2178 , HOH A:2201 , HOH A:3056
BINDING SITE FOR RESIDUE GOL A1722
02
AC2
SOFTWARE
TYR A:50 , ASP A:65 , THR A:67 , TYR A:68
BINDING SITE FOR RESIDUE PGE A1723
03
AC3
SOFTWARE
PRO A:27 , ASP A:65 , HOH A:2138 , HOH A:3057 , HOH A:3058
BINDING SITE FOR RESIDUE PGE A1724
04
AC4
SOFTWARE
ALA A:395 , GLU A:396 , THR A:399 , HOH A:2218 , HOH A:3059 , HOH A:3060 , HOH A:3061
BINDING SITE FOR RESIDUE PGE A1725
05
AC5
SOFTWARE
ARG A:456 , ASP A:501 , HOH A:3062 , HOH A:3063 , HOH A:3064 , HOH A:3065
BINDING SITE FOR RESIDUE PGE A1726
06
AC6
SOFTWARE
ARG A:111 , TYR A:115 , ARG A:116 , ARG A:164 , HOH A:3067 , HOH A:3069
BINDING SITE FOR RESIDUE PO4 A1727
07
AC7
SOFTWARE
GLN A:187 , GLY A:188 , LYS A:263 , ASN A:267 , GLN A:268 , THR A:269
BINDING SITE FOR RESIDUE NA A1728
08
AC8
SOFTWARE
GLN A:75 , PRO A:78 , SER A:79 , THR A:82 , ASP A:84
BINDING SITE FOR RESIDUE NA A1729
09
AC9
SOFTWARE
TYR A:253 , TYR A:493 , VAL A:496 , LEU A:497
BINDING SITE FOR RESIDUE NA A1730
10
BC1
SOFTWARE
PHE A:195 , TYR A:196 , GLY A:197 , ARG A:203 , HIS A:226 , NA A:1750
BINDING SITE FOR RESIDUE NA A1731
11
BC2
SOFTWARE
SER A:519 , GLY A:521 , GLY A:522 , GLY A:523 , ARG A:524 , PHE A:525 , ILE A:536 , NA A:1751
BINDING SITE FOR RESIDUE NA A1732
12
BC3
SOFTWARE
ALA A:72 , LEU A:73 , PRO A:74 , ARG A:86 , GLN A:268 , HOH A:2367
BINDING SITE FOR RESIDUE NA A1733
13
BC4
SOFTWARE
GLY A:57 , GLY A:83 , TYR A:85 , NA A:1752
BINDING SITE FOR RESIDUE NA A1734
14
BC5
SOFTWARE
HIS A:33 , GLN A:75 , CYS A:182 , LEU A:183 , ASP A:184
BINDING SITE FOR RESIDUE NA A1735
15
BC6
SOFTWARE
ARG A:194 , GLY A:211 , HIS A:212 , GLY A:213 , THR A:214 , HOH A:2387
BINDING SITE FOR RESIDUE NA A1736
16
BC7
SOFTWARE
GLY A:218 , SER A:219 , SER A:225 , GLN A:227 , TYR A:228 , HOH A:2437
BINDING SITE FOR RESIDUE NA A1737
17
BC8
SOFTWARE
ASP A:71 , ARG A:86 , ASP A:264 , GLN A:265 , HOH A:2165
BINDING SITE FOR RESIDUE NA A1738
18
BC9
SOFTWARE
HIS A:212 , TYR A:228 , LYS A:263 , ASP A:264 , GLN A:265 , HOH A:2445
BINDING SITE FOR RESIDUE NA A1739
19
CC1
SOFTWARE
PHE A:55 , THR A:223 , SER A:482 , HOH A:2444 , HOH A:2816
BINDING SITE FOR RESIDUE NA A1740
20
CC2
SOFTWARE
THR A:49 , ALA A:72 , LEU A:73 , HOH A:2125 , HOH A:2154 , HOH A:2166
BINDING SITE FOR RESIDUE NA A1741
21
CC3
SOFTWARE
ARG A:547 , GLN A:551 , ALA A:565 , ALA A:588 , HOH A:2840 , HOH A:2870
BINDING SITE FOR RESIDUE NA A1742
22
CC4
SOFTWARE
GLU A:176 , GLU A:277 , PHE A:280 , HOH A:2520 , HOH A:2521
BINDING SITE FOR RESIDUE NA A1743
23
CC5
SOFTWARE
SER A:224 , SER A:225 , ASN A:229 , GLY A:523 , ARG A:524 , PHE A:525 , NA A:1750
BINDING SITE FOR RESIDUE NA A1744
24
CC6
SOFTWARE
LEU A:31 , GLN A:75 , GLU A:76 , TYR A:77 , HOH A:2171
BINDING SITE FOR RESIDUE NA A1745
25
CC7
SOFTWARE
TYR A:552 , ARG A:631 , SER A:633 , ALA A:642 , HOH A:2934 , HOH A:2952
BINDING SITE FOR RESIDUE NA A1746
26
CC8
SOFTWARE
VAL A:586 , MET A:589 , SER A:656 , GLN A:714 , HOH A:2872
BINDING SITE FOR RESIDUE NA A1747
27
CC9
SOFTWARE
TYR A:85 , SER A:219 , ARG A:220 , HOH A:2437
BINDING SITE FOR RESIDUE NA A1748
28
DC1
SOFTWARE
SER A:258 , GLU A:260 , LEU A:272 , HOH A:2514
BINDING SITE FOR RESIDUE NA A1749
29
DC2
SOFTWARE
ARG A:203 , SER A:225 , ASN A:229 , NA A:1731 , NA A:1744
BINDING SITE FOR RESIDUE NA A1750
30
DC3
SOFTWARE
GLY A:517 , CYS A:518 , ARG A:524 , ILE A:536 , NA A:1732 , HOH A:2815
BINDING SITE FOR RESIDUE NA A1751
31
DC4
SOFTWARE
TYR A:85 , VAL A:440 , ARG A:481 , SER A:482 , NA A:1734 , HOH A:2733
BINDING SITE FOR RESIDUE NA A1752
32
DC5
SOFTWARE
HIS A:199 , ALA A:200 , GLU A:202 , GLY A:520 , SER A:539 , ASP A:540
BINDING SITE FOR RESIDUE NA A1753
33
DC6
SOFTWARE
LEU A:250 , PHE A:251 , ASP A:526 , ALA A:527 , TYR A:558
BINDING SITE FOR RESIDUE NA A1754
34
DC7
SOFTWARE
TRP A:336 , ASP A:366 , ASP A:367 , TRP A:411 , ARG A:443 , LYS A:476 , ASP A:478 , ASN A:480 , CYS A:518 , GLY A:520 , GLY A:521 , TRP A:537 , ASP A:540 , HOH A:3070 , HOH A:3071
BINDING SITE FOR RESIDUE GLA A1755
35
DC8
SOFTWARE
TRP A:336 , ASP A:366 , ASP A:367 , TRP A:411 , ARG A:443 , LYS A:476 , ASP A:478 , ASN A:480 , CYS A:518 , GLY A:520 , GLY A:521 , TRP A:537 , ASP A:540 , HOH A:3070
BINDING SITE FOR RESIDUE GAL A1756
[
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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: ALPHA_GALACTOSIDASE (A:359-374)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ALPHA_GALACTOSIDASE
PS00512
Alpha-galactosidase signature.
AGASK_RUMGN
359-374
1
A:359-374
[
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
(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 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 (267 KB)
Header - Asym.Unit
Biol.Unit 1 (1022 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
2YFO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
