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.
1J0D
Biol. Unit 1
Info
Asym.Unit (238 KB)
Biol.Unit 1 (114 KB)
Biol.Unit 2 (122 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ACC DEAMINASE MUTANT COMPLEXED WITH ACC
Authors
:
T. Ose, A. Fujino, M. Yao, M. Honma, I. Tanaka
Date
:
12 Nov 02 (Deposition) - 12 May 03 (Release) - 24 Feb 09 (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
:
Plp Dependent B Group, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Ose, A. Fujino, M. Yao, N. Watanabe, M. Honma, I. Tanaka
Reaction Intermediate Structures Of 1-Aminocyclopropane-1-Carboxylate Deaminase: Insight Into Plp-Dependent Cyclopropane Ring-Opening Reaction
J. Biol. Chem. V. 278 41069 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: N-[3-HYDROXY-2-METHYL-5-PHOSPHONOO... (5PAa)
1b: N-[3-HYDROXY-2-METHYL-5-PHOSPHONOO... (5PAb)
1c: N-[3-HYDROXY-2-METHYL-5-PHOSPHONOO... (5PAc)
1d: N-[3-HYDROXY-2-METHYL-5-PHOSPHONOO... (5PAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
5PA
2
Ligand/Ion
N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-Y-LMETHYL]-1-AMINO-CYCLOPROPANECARBOXYLIC ACID
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:54 , GLY A:74 , GLY A:75 , SER A:78 , ASN A:79 , GLN A:80 , TRP A:102 , ALA A:163 , GLY A:164 , SER A:166 , CYS A:200 , VAL A:201 , THR A:202 , GLY A:203 , SER A:204 , THR A:205 , TYR A:295 , GLU A:296 , HOH A:1467 , HOH A:1477
BINDING SITE FOR RESIDUE 5PA A 1401
2
AC2
SOFTWARE
ASN B:50 , LYS B:54 , SER B:78 , ASN B:79 , GLN B:80 , GLY B:164 , CYS B:200 , VAL B:201 , THR B:202 , GLY B:203 , SER B:204 , THR B:205 , TYR B:295 , GLU B:296 , LEU B:323 , GLY B:324 , GLY B:325 , HOH B:1507 , HOH B:1574
BINDING SITE FOR RESIDUE 5PA B 1501
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1j0da_ (A:)
1b: SCOP_d1j0db_ (B:)
1c: SCOP_d1j0dc_ (C:)
1d: SCOP_d1j0dd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Tryptophan synthase beta subunit-like PLP-dependent enzymes
(165)
Superfamily
:
Tryptophan synthase beta subunit-like PLP-dependent enzymes
(165)
Family
:
Tryptophan synthase beta subunit-like PLP-dependent enzymes
(120)
Protein domain
:
1-aminocyclopropane-1-carboxylate deaminase
(12)
Yeast (Hansenula saturnus) [TaxId: 4906]
(4)
1a
d1j0da_
A:
1b
d1j0db_
B:
1c
d1j0dc_
C:
1d
d1j0dd_
D:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1j0dA01 (A:1-45,A:168-341)
1b: CATH_1j0dA02 (A:66-167)
1c: CATH_1j0dB02 (B:66-167)
1d: CATH_1j0dC02 (C:66-167)
1e: CATH_1j0dD02 (D:66-167)
1f: CATH_1j0dB01 (B:1-45,B:168-341)
1g: CATH_1j0dC01 (C:1-45,C:168-341)
1h: CATH_1j0dD01 (D:1-45,D:168-341)
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=3.40.50.1100, no name defined]
(77)
Williopsis saturnus. Organism_taxid: 4906.
(4)
1a
1j0dA01
A:1-45,A:168-341
1b
1j0dA02
A:66-167
1c
1j0dB02
B:66-167
1d
1j0dC02
C:66-167
1e
1j0dD02
D:66-167
1f
1j0dB01
B:1-45,B:168-341
1g
1j0dC01
C:1-45,C:168-341
1h
1j0dD01
D:1-45,D:168-341
[
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
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 (114 KB)
Header - Biol.Unit 1
Biol.Unit 2 (122 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
1J0D
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help