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.
1KWG
Biol. Unit 1
Info
Asym.Unit (123 KB)
Biol.Unit 1 (348 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 THERMUS THERMOPHILUS A4 BETA-GALACTOSIDASE
Authors
:
M. Hidaka, S. Fushinobu, N. Ohtsu, H. Motoshima, H. Matsuzawa, H. Shoun
Date
:
29 Jan 02 (Deposition) - 18 Sep 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A
Biol. Unit 1: A (3x)
Keywords
:
Tim Barrel, Glycoside Hydrolase Family 42, Trimer, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Hidaka, S. Fushinobu, N. Ohtsu, H. Motoshima, H. Matsuzawa, H. Shoun, T. Wakagi
Trimeric Crystal Structure Of The Glycoside Hydrolase Famil 42 Beta-Galactosidase From Thermus Thermophilus A4 And The Structure Of Its Complex With Galactose
J. Mol. Biol. V. 322 79 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 12)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
2a: CHLORIDE ION (CLa)
3a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
3b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
4a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
6
Ligand/Ion
ACETATE ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
MPD
6
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
4
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:6 , TYR A:7 , TRP A:11 , ARG A:351 , ARG A:353
BINDING SITE FOR RESIDUE CL A 801
2
AC2
SOFTWARE
GLY A:535 , HOH A:875 , HOH A:927 , HOH A:1424
BINDING SITE FOR RESIDUE ACT A 804
3
AC3
SOFTWARE
ARG A:560
BINDING SITE FOR RESIDUE ACT A 805
4
AC4
SOFTWARE
CYS A:106 , CYS A:150 , CYS A:152 , CYS A:155
BINDING SITE FOR RESIDUE ZN A 806
5
AC5
SOFTWARE
PRO A:275
BINDING SITE FOR RESIDUE MPD A 802
6
AC6
SOFTWARE
ALA A:433 , ARG A:436 , PRO A:573 , GLY A:577 , HOH A:865 , HOH A:902 , HOH A:984
BINDING SITE FOR RESIDUE MPD A 803
[
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
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1kwga1 (A:591-644)
2a: SCOP_d1kwga3 (A:394-590)
3a: SCOP_d1kwga2 (A:1-393)
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
:
A4 beta-galactosidase
(2)
Thermus thermophilus [TaxId: 274]
(2)
1a
d1kwga1
A:591-644
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Class I glutamine amidotransferase-like
(173)
Family
:
A4 beta-galactosidase middle domain
(2)
Protein domain
:
A4 beta-galactosidase middle domain
(2)
Thermus thermophilus [TaxId: 274]
(2)
2a
d1kwga3
A:394-590
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
Amylase, catalytic domain
(385)
Protein domain
:
A4 beta-galactosidase
(2)
Thermus thermophilus [TaxId: 274]
(2)
3a
d1kwga2
A:1-393
[
close SCOP info
]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_1kwgA02 (A:395-594)
2a: CATH_1kwgA01 (A:1-394)
3a: CATH_1kwgA03 (A:595-644)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.880, no name defined]
(97)
Thermus thermophilus. Organism_taxid: 274. Strain: a4.
(2)
1a
1kwgA02
A:395-594
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
Thermus thermophilus. Organism_taxid: 274. Strain: a4.
(2)
2a
1kwgA01
A:1-394
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Golgi alpha-mannosidase II
(346)
Thermus thermophilus. Organism_taxid: 274. Strain: a4.
(2)
3a
1kwgA03
A:595-644
[
close CATH info
]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_42C_1kwgA01 (A:597-644)
2a: PFAM_Glyco_hydro_42M_1kwgA02 (A:398-590)
3a: PFAM_Glyco_hydro_42_1kwgA03 (A:5-390)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GHD
(106)
Family
:
Glyco_hydro_42C
(2)
Thermus thermophilus
(2)
1a
Glyco_hydro_42C-1kwgA01
A:597-644
Clan
:
Glutaminase_I
(73)
Family
:
Glyco_hydro_42M
(2)
Thermus thermophilus
(2)
2a
Glyco_hydro_42M-1kwgA02
A:398-590
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_42
(2)
Thermus thermophilus
(2)
3a
Glyco_hydro_42-1kwgA03
A:5-390
[
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
Asymmetric Unit 2
Asymmetric Unit 3
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 (123 KB)
Header - Asym.Unit
Biol.Unit 1 (348 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
1KWG
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
