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.
4ADB
Biol. Unit 2
Info
Asym.Unit (270 KB)
Biol.Unit 1 (136 KB)
Biol.Unit 2 (133 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURAL AND FUNCTIONAL STUDY OF SUCCINYL-ORNITHINE TRANSAMINASE FROM E. COLI
Authors
:
J. Newman, T. S. Peat
Date
:
23 Dec 11 (Deposition) - 16 Jan 13 (Release) - 27 Mar 13 (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
:
Transferase, Plp Enzymes, Aminotransferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Newman, S. Seabrook, R. Surjadi, C. C. Williams, D. Lucent, M. Wilding, C. Scott, T. S. Peat
Determination Of The Structure Of The Catabolic N- Succinylornithine Transaminase (Astc) From Escherichia Coli
Plos One V. 8 58298 2013
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
2c: SODIUM ION (NAc)
2d: SODIUM ION (NAd)
3a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
3b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
3c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
3d: PYRIDOXAL-5'-PHOSPHATE (PLPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
NA
-1
Ligand/Ion
SODIUM ION
3
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC6 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
5: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
HOH A:2110 , HOH A:2111 , HOH A:2220 , HOH A:2221 , HOH A:2222 , HOH A:2223 , LYS C:118
BINDING SITE FOR RESIDUE MG A1999
2
AC6
SOFTWARE
SER C:104 , GLY C:105 , ALA C:106 , PHE C:138 , HIS C:139 , GLU C:190 , ASP C:223 , VAL C:225 , GLN C:226 , LYS C:252 , HOH C:2094 , HOH C:2123 , HOH C:2153 , HOH C:2154 , HOH C:2155 , THR D:281
BINDING SITE FOR RESIDUE PLP C1404
3
AC7
SOFTWARE
THR C:281 , HOH C:2073 , HOH C:2130 , SER D:104 , GLY D:105 , ALA D:106 , PHE D:138 , HIS D:139 , GLU D:190 , ASP D:223 , VAL D:225 , GLN D:226 , LYS D:252 , HOH D:2051 , HOH D:2085
BINDING SITE FOR RESIDUE PLP D1404
4
AC8
SOFTWARE
ILE C:91 , THR C:94 , ALA C:96 , HOH C:2063 , HOH C:2065
BINDING SITE FOR RESIDUE NA C1405
5
BC1
SOFTWARE
ILE D:91 , THR D:94 , PHE D:95 , ALA D:96
BINDING SITE FOR RESIDUE NA D1405
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: AA_TRANSFER_CLASS_3 (C:220-257,D:220-257)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AA_TRANSFER_CLASS_3
PS00600
Aminotransferases class-III pyridoxal-phosphate attachment site.
ASTC_ECOLI
220-257
2
-
-
C:220-257
D:220-257
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d4adba_ (A:)
1b: SCOP_d4adbb_ (B:)
1c: SCOP_d4adbc_ (C:)
1d: SCOP_d4adbd_ (D:)
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
:
automated matches
(163)
Protein domain
:
automated matches
(163)
Escherichia coli [TaxId: 511693]
(4)
1a
d4adba_
A:
1b
d4adbb_
B:
1c
d4adbc_
C:
1d
d4adbd_
D:
[
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 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 (270 KB)
Header - Asym.Unit
Biol.Unit 1 (136 KB)
Header - Biol.Unit 1
Biol.Unit 2 (133 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
4ADB
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help