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.
3PGQ
Asym. Unit
Info
Asym.Unit (710 KB)
Biol.Unit 1 (469 KB)
Biol.Unit 2 (469 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 THE CARBOXYLTRANSFERASE DOMAIN OF S. CEREVISIAE ACETYL COA CARBOXYLASE IN COMPLEX WITH PINOXADEN
Authors
:
L. Tong, L. P. C. Yu, Y. S. Kim
Date
:
02 Nov 10 (Deposition) - 22 Dec 10 (Release) - 05 Jan 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (2x)
Biol. Unit 2: B,C (1x)
Keywords
:
Transferase, Carboxyltransferase, Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. P. Yu, Y. S. Kim, L. Tong
Mechanism For The Inhibition Of The Carboxyltransferase Domain Of Acetyl-Coenzyme A Carboxylase By Pinoxaden.
Proc. Natl. Acad. Sci. Usa V. 107 22072 2010
[
close entry info
]
Hetero Components
(1, 3)
Info
All Hetero Components
1a: 8-(2-ETHENYL-6-ETHYL-4-METHYLPHENY... (GY3a)
1b: 8-(2-ETHENYL-6-ETHYL-4-METHYLPHENY... (GY3b)
1c: 8-(2-ETHENYL-6-ETHYL-4-METHYLPHENY... (GY3c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GY3
3
Ligand/Ion
8-(2-ETHENYL-6-ETHYL-4-METHYLPHENYL)TETRAHYDRO-7H-PYRAZOLO[1,2-D][1,4,5]OXADIAZEPINE-7,9(8H)-DIONE
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:1625 , GLY A:1626 , ALA A:1627 , LEU A:1705 , SER A:1708 , GLY A:1734 , ILE A:1735 , TYR A:1738 , LEU A:1756 , GLY A:1997 , GLY A:1998 , VAL A:2001 , LEU A:2025
BINDING SITE FOR RESIDUE GY3 A 3000
2
AC2
SOFTWARE
GLY B:1626 , ALA B:1627 , LEU B:1705 , SER B:1708 , GLY B:1734 , ILE B:1735 , TYR B:1738 , GLY C:1997 , GLY C:1998 , VAL C:2001 , LEU C:2025
BINDING SITE FOR RESIDUE GY3 B 3000
3
AC3
SOFTWARE
GLY B:1997 , GLY B:1998 , VAL B:2001 , LEU B:2025 , GLY C:1626 , ALA C:1627 , LEU C:1705 , SER C:1708 , GLY C:1734 , ILE C:1735 , TYR C:1738 , LEU C:1756
BINDING SITE FOR RESIDUE GY3 B 2240
[
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
(2, 5)
Info
All PROSITE Patterns/Profiles
1: COA_CT_NTER (A:1486-1822,B:1486-1822)
2: COA_CT_CTER (A:1826-2141,B:1826-2141,C:1826-214...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
COA_CT_NTER
PS50980
Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile.
ACAC_YEAST
1486-1822
2
A:1486-1822
B:1486-1822
2
COA_CT_CTER
PS50989
Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile.
ACAC_YEAST
1826-2141
3
A:1826-2141
B:1826-2141
C:1826-2141
[
close PROSITE info
]
Exons
(1, 3)
Info
All Exons
Exon 1.1 (A:1480-2195 (gaps) | B:1480-2192 (...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
YNR016C
1
YNR016C.1
XIV:661377-654676
6702
ACAC_YEAST
1-2233
2233
3
A:1480-2195 (gaps)
B:1480-2192 (gaps)
C:1491-2193 (gaps)
716
713
703
[
close EXON info
]
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d3pgqa1 (A:1480-1814)
1b: SCOP_d3pgqa2 (A:1815-2195)
1c: SCOP_d3pgqb1 (B:1480-1814)
1d: SCOP_d3pgqb2 (B:1815-2192)
1e: SCOP_d3pgqc1 (C:1491-1814)
1f: SCOP_d3pgqc2 (C:1815-2193)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
ClpP/crotonase
(207)
Superfamily
:
ClpP/crotonase
(207)
Family
:
Biotin dependent carboxylase carboxyltransferase domain
(32)
Protein domain
:
automated matches
(9)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(4)
1a
d3pgqa1
A:1480-1814
1b
d3pgqa2
A:1815-2195
1c
d3pgqb1
B:1480-1814
1d
d3pgqb2
B:1815-2192
1e
d3pgqc1
C:1491-1814
1f
d3pgqc2
C:1815-2193
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_Carboxyl_trans_3pgqC01 (C:1574-2130)
1b: PFAM_Carboxyl_trans_3pgqC02 (C:1574-2130)
1c: PFAM_Carboxyl_trans_3pgqC03 (C:1574-2130)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
ClpP_crotonase
(88)
Family
:
Carboxyl_trans
(13)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(9)
1a
Carboxyl_trans-3pgqC01
C:1574-2130
1b
Carboxyl_trans-3pgqC02
C:1574-2130
1c
Carboxyl_trans-3pgqC03
C:1574-2130
[
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
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 (710 KB)
Header - Asym.Unit
Biol.Unit 1 (469 KB)
Header - Biol.Unit 1
Biol.Unit 2 (469 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
3PGQ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
