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.
4KGZ
Biol. Unit 1
Info
Asym.Unit (319 KB)
Biol.Unit 1 (918 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE R STATE STRUCTURE OF E. COLI ATCASE WITH UTP AND MAGNESIUM BOUND
Authors
:
G. M. Cockrell, Y. Zheng, W. Guo, A. W. Peterson, E. R. Kantrowitz
Date
:
29 Apr 13 (Deposition) - 27 Nov 13 (Release) - 27 Nov 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (3x)
Keywords
:
Pyrimidine Nucleotide Biosynthesis, Feedback Inhibition, Competing Pathway Product Activation, Allostery, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. M. Cockrell, Y. Zheng, W. Guo, A. W. Peterson, J. K. Truong, E. R. Kantrowitz
New Paradigm For Allosteric Regulation Of Escherichia Coli Aspartate Transcarbamoylase.
Biochemistry V. 52 8036 2013
[
close entry info
]
Hetero Components
(2, 18)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
2a: N-(PHOSPHONACETYL)-L-ASPARTIC ACID (PALa)
2b: N-(PHOSPHONACETYL)-L-ASPARTIC ACID (PALb)
3a: URIDINE 5'-TRIPHOSPHATE (UTPa)
3b: URIDINE 5'-TRIPHOSPHATE (UTPb)
3c: URIDINE 5'-TRIPHOSPHATE (UTPc)
3d: URIDINE 5'-TRIPHOSPHATE (UTPd)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
PAL
6
Ligand/Ion
N-(PHOSPHONACETYL)-L-ASPARTIC ACID
3
UTP
12
Ligand/Ion
URIDINE 5'-TRIPHOSPHATE
4
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:52 , THR A:53 , ARG A:54 , THR A:55 , SER A:80 , LYS A:84 , ARG A:105 , HIS A:134 , ARG A:167 , ARG A:229 , GLN A:231 , LEU A:267 , HOH A:506 , HOH A:538
BINDING SITE FOR RESIDUE PAL A 401
02
AC2
SOFTWARE
CYS B:109 , CYS B:114 , CYS B:138 , CYS B:141
BINDING SITE FOR RESIDUE ZN B 201
03
AC3
SOFTWARE
ALA B:11 , ILE B:12 , VAL B:17 , HIS B:20 , LYS B:60 , TYR B:89 , LYS B:94 , UTP B:203 , MG B:204 , HOH B:301 , HOH B:302
BINDING SITE FOR RESIDUE UTP B 202
04
AC4
SOFTWARE
GLU B:10 , HIS B:20 , LEU B:48 , PRO B:49 , SER B:50 , GLU B:52 , LYS B:56 , LYS B:60 , UTP B:202 , MG B:204 , HOH B:301 , HOH B:302 , ARG D:41
BINDING SITE FOR RESIDUE UTP B 203
05
AC5
SOFTWARE
UTP B:202 , UTP B:203 , HOH B:301 , HOH B:302
BINDING SITE FOR RESIDUE MG B 204
06
AC6
SOFTWARE
SER C:52 , THR C:53 , ARG C:54 , THR C:55 , SER C:80 , LYS C:84 , ARG C:105 , HIS C:134 , ARG C:167 , THR C:168 , ARG C:229 , GLN C:231 , LEU C:267 , HOH C:509 , HOH C:528 , HOH C:531
BINDING SITE FOR RESIDUE PAL C 401
07
AC7
SOFTWARE
CYS D:109 , CYS D:114 , CYS D:138 , CYS D:141
BINDING SITE FOR RESIDUE ZN D 201
08
AC8
SOFTWARE
ALA D:11 , ILE D:12 , HIS D:20 , LYS D:60 , TYR D:89 , LYS D:94 , UTP D:203 , MG D:204 , HOH D:301 , HOH D:302 , HOH D:318
BINDING SITE FOR RESIDUE UTP D 202
09
AC9
SOFTWARE
ARG B:41 , HIS D:20 , LEU D:48 , PRO D:49 , SER D:50 , GLY D:51 , GLU D:52 , LYS D:56 , LEU D:58 , LYS D:60 , UTP D:202 , MG D:204 , HOH D:301 , HOH D:302
BINDING SITE FOR RESIDUE UTP D 203
10
BC1
SOFTWARE
UTP D:202 , UTP D:203 , HOH D:301 , HOH D:302
BINDING SITE FOR RESIDUE MG D 204
[
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, 8)
Info
All SCOP Domains
1a: SCOP_d4kgzb1 (B:10-100)
1b: SCOP_d4kgzd1 (D:11-100)
2a: SCOP_d4kgza1 (A:1-150)
2b: SCOP_d4kgza2 (A:151-310)
2c: SCOP_d4kgzc1 (C:1-150)
2d: SCOP_d4kgzc2 (C:151-310)
3a: SCOP_d4kgzb2 (B:101-153)
3b: SCOP_d4kgzd2 (D:101-153)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
(63)
Family
:
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
(62)
Protein domain
:
Aspartate carbamoyltransferase
(62)
Escherichia coli [TaxId: 562]
(59)
1a
d4kgzb1
B:10-100
1b
d4kgzd1
D:11-100
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
ATC-like
(129)
Superfamily
:
Aspartate/ornithine carbamoyltransferase
(122)
Family
:
Aspartate/ornithine carbamoyltransferase
(87)
Protein domain
:
Aspartate carbamoyltransferase catalytic subunit
(68)
Escherichia coli [TaxId: 562]
(62)
2a
d4kgza1
A:1-150
2b
d4kgza2
A:151-310
2c
d4kgzc1
C:1-150
2d
d4kgzc2
C:151-310
Class
:
Small proteins
(3458)
Fold
:
Rubredoxin-like
(572)
Superfamily
:
Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain
(63)
Family
:
Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain
(62)
Protein domain
:
Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain
(62)
Escherichia coli [TaxId: 562]
(59)
3a
d4kgzb2
B:101-153
3b
d4kgzd2
D:101-153
[
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 A
Chain B
Chain C
Chain D
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 (319 KB)
Header - Asym.Unit
Biol.Unit 1 (918 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
4KGZ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help