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.
3LRK
Asym. Unit
Info
Asym.Unit (89 KB)
Biol.Unit 1 (324 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 ALFA-GALACTOSIDASE (MEL1) FROM SACCHAROMYCES CEREVISIAE
Authors
:
R. Fernandez-Leiro, A. Pereira-Rodriguez, M. E. Cerdan, M. Becerra, J Aparicio
Date
:
11 Feb 10 (Deposition) - 30 Jun 10 (Release) - 26 Jan 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A
Biol. Unit 1: A (4x)
Keywords
:
Alpha-Galactosidase, Tetramer, Gh27, Glycoprotein, Glycosidase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Fernandez-Leiro, A. Pereira-Rodriguez, M. E. Cerdan, M. Becerra, J. Sanz-Aparicio
Structural Analysis Of Saccharomyces Cerevisiae Alpha-Galactosidase And Its Complexes With Natural Substrates Reveals New Insights Into Substrate Specificity Of Gh27 Glycosidases.
J. Biol. Chem. V. 285 28020 2010
[
close entry info
]
Hetero Components
(4, 13)
Info
All Hetero Components
1a: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-... (BTBa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3a: SODIUM ION (NAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BTB
1
Ligand/Ion
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2
GOL
3
Ligand/Ion
GLYCEROL
3
NA
1
Ligand/Ion
SODIUM ION
4
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:82 , HIS A:102 , ASN A:105 , GLU A:133 , HOH A:566 , HOH A:640 , HOH A:655 , HOH A:712 , HOH A:885
BINDING SITE FOR RESIDUE NAG A 1001
02
AC2
SOFTWARE
ASN A:175 , GLY A:178 , HOH A:628 , HOH A:859
BINDING SITE FOR RESIDUE NAG A 2001
03
AC3
SOFTWARE
GLY A:267 , GLY A:269 , ASN A:270 , LEU A:382 , HOH A:487 , HOH A:598 , NAG A:3002
BINDING SITE FOR RESIDUE NAG A 3001
04
AC4
SOFTWARE
ASN A:298 , HOH A:598 , HOH A:629 , NAG A:3001
BINDING SITE FOR RESIDUE NAG A 3002
05
AC5
SOFTWARE
ASP A:273 , SER A:302 , ASN A:403 , HOH A:586 , HOH A:588 , HOH A:684 , HOH A:729
BINDING SITE FOR RESIDUE NAG A 4001
06
AC6
SOFTWARE
ASP A:63 , THR A:417 , ASN A:422 , HOH A:686 , HOH A:805 , NAG A:5002
BINDING SITE FOR RESIDUE NAG A 5001
07
AC7
SOFTWARE
SER A:107 , HOH A:805 , NAG A:5001
BINDING SITE FOR RESIDUE NAG A 5002
08
AC8
SOFTWARE
TRP A:328 , TYR A:330 , ASN A:370
BINDING SITE FOR RESIDUE NAG A 6001
09
AC9
SOFTWARE
TRP A:37 , ASP A:72 , ASP A:73 , CYS A:121 , ALA A:122 , LYS A:147 , ASP A:149 , HOH A:887 , HOH A:888
BINDING SITE FOR RESIDUE GOL A 7001
10
BC1
SOFTWARE
ASP A:35 , TRP A:37 , ASN A:38 , LYS A:147 , ARG A:205 , VAL A:210 , ASP A:262 , ASN A:263 , HOH A:525 , HOH A:626 , HOH A:868
BINDING SITE FOR RESIDUE GOL A 7002
11
BC2
SOFTWARE
MET A:64 , SER A:308 , GLN A:309 , ALA A:310 , ASN A:399 , LEU A:420 , TYR A:421 , HOH A:508
BINDING SITE FOR RESIDUE GOL A 7003
12
BC3
SOFTWARE
HIS A:98 , HIS A:102 , BTB A:9001
BINDING SITE FOR RESIDUE NA A 8001
13
BC4
SOFTWARE
GLU A:46 , SER A:81 , ASP A:82 , ASN A:94 , HIS A:98 , HIS A:102 , NA A:8001
BINDING SITE FOR RESIDUE BTB A 9001
[
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:65-80)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ALPHA_GALACTOSIDASE
PS00512
Alpha-galactosidase signature.
MEL1_YEASX
65-80
1
A:65-80
[
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
(1, 1)
Info
all PFAM domains
1a: PFAM_Melibiase_3lrkA01 (A:19-363)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Glyco_hydro_tim
(488)
Family
:
Melibiase
(11)
Saccharomyces cerevisiae (Bakers yeast)
(3)
1a
Melibiase-3lrkA01
A:19-363
[
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 (89 KB)
Header - Asym.Unit
Biol.Unit 1 (324 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
3LRK
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help