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.
5BJ3
Asym. Unit
Info
Asym.Unit (238 KB)
Biol.Unit 1 (119 KB)
Biol.Unit 2 (119 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 1
Authors
:
H. Ura, T. Nakai, S. I. Kawaguchi, I. Miyahara, K. Hirotsu, S. Kuramitsu
Date
:
11 Jan 99 (Deposition) - 02 Sep 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Aminotransferase, Pyridoxal Enzyme, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Ura, T. Nakai, S. I. Kawaguchi, I. Miyahara, K. Hirotsu, S. Kuramits
Substrate Recognition Mechanism Of Thermophilic Dual-Substrate Enzyme
J. Biochem. (Tokyo) V. 130 89 2001
[
close entry info
]
Hetero Components
(1, 4)
Info
All Hetero Components
1a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
1b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
1c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
1d: PYRIDOXAL-5'-PHOSPHATE (PLPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PLP
4
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:99 , GLY A:100 , SER A:101 , TRP A:125 , ASN A:171 , ASN A:175 , ASP A:203 , ILE A:205 , TYR A:206 , ALA A:233 , LYS A:234 , ARG A:242 , TYR B:64
BINDING SITE FOR RESIDUE PLP A 413
2
AC2
SOFTWARE
TYR A:64 , GLY B:99 , GLY B:100 , SER B:101 , TRP B:125 , ASN B:171 , ASN B:175 , ASP B:203 , ILE B:205 , TYR B:206 , ALA B:233 , LYS B:234 , ARG B:242
BINDING SITE FOR RESIDUE PLP B 413
3
AC3
SOFTWARE
GLY C:99 , GLY C:100 , SER C:101 , TRP C:125 , ASN C:171 , ASN C:175 , ASP C:203 , ILE C:205 , TYR C:206 , ALA C:233 , LYS C:234 , ARG C:242 , HOH C:431 , TYR D:64
BINDING SITE FOR RESIDUE PLP C 413
4
AC4
SOFTWARE
TYR C:64 , HOH C:430 , GLY D:99 , GLY D:100 , SER D:101 , TRP D:125 , ASN D:171 , ASN D:175 , ASP D:203 , ILE D:205 , TYR D:206 , ALA D:233 , LYS D:234 , ARG D:242 , HOH D:450
BINDING SITE FOR RESIDUE PLP D 413
[
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
(0, 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.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d5bj3a_ (A:)
1b: SCOP_d5bj3c_ (C:)
1c: SCOP_d5bj3d_ (D:)
1d: SCOP_d5bj3b_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PLP-dependent transferase-like
(627)
Superfamily
:
PLP-dependent transferases
(625)
Family
:
AAT-like
(184)
Protein domain
:
Aspartate aminotransferase, AAT
(112)
Thermus thermophilus [TaxId: 274]
(9)
1a
d5bj3a_
A:
1b
d5bj3c_
C:
1c
d5bj3d_
D:
1d
d5bj3b_
B:
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_5bj3A02 (A:63-281)
1b: CATH_5bj3B02 (B:63-281)
1c: CATH_5bj3C02 (C:63-281)
1d: CATH_5bj3D02 (D:63-281)
2a: CATH_5bj3A01 (A:1-62,A:282-381)
2b: CATH_5bj3B01 (B:1-62,B:282-381)
2c: CATH_5bj3C01 (C:1-62,C:282-381)
2d: CATH_5bj3D01 (D:1-62,D:282-381)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aspartate Aminotransferase; domain 2
(384)
Homologous Superfamily
:
Type I PLP-dependent aspartate aminotransferase-like (Major domain)
(384)
Thermus aquaticus. Organism_taxid: 271. Strain: hb8.
(1)
1a
5bj3A02
A:63-281
1b
5bj3B02
B:63-281
1c
5bj3C02
C:63-281
1d
5bj3D02
D:63-281
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aspartate Aminotransferase, domain 1
(355)
Homologous Superfamily
:
Aspartate Aminotransferase, domain 1
(354)
Thermus aquaticus. Organism_taxid: 271. Strain: hb8.
(1)
2a
5bj3A01
A:1-62,A:282-381
2b
5bj3B01
B:1-62,B:282-381
2c
5bj3C01
C:1-62,C:282-381
2d
5bj3D01
D:1-62,D:282-381
[
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
Chain B
Chain C
Chain D
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 (238 KB)
Header - Asym.Unit
Biol.Unit 1 (119 KB)
Header - Biol.Unit 1
Biol.Unit 2 (119 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
5BJ3
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help