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.
4JX5
Asym. Unit
Info
Asym.Unit (769 KB)
Biol.Unit 1 (758 KB)
Biol.Unit 2 (386 KB)
Biol.Unit 3 (380 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE CARBOXYL TRANSFERASE DOMAIN FROM RHIZOBIUM ETLI PYRUVATE CARBOXYLASE WITH PYRUVATE
Authors
:
A. D. Lietzan, M. St Maurice
Date
:
27 Mar 13 (Deposition) - 29 May 13 (Release) - 24 Jul 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.55
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,C (1x)
Biol. Unit 3: B,D (1x)
Keywords
:
Tim Barrel, Ligase, Ligase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. D. Lietzan, M. St Maurice
A Substrate-Induced Biotin Binding Pocket In The Carboxyltransferase Domain Of Pyruvate Carboxylase.
J. Biol. Chem. V. 288 19915 2013
[
close entry info
]
Hetero Components
(6, 22)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
3b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
3c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
3d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
5a: PYRUVIC ACID (PYRa)
5b: PYRUVIC ACID (PYRb)
5c: PYRUVIC ACID (PYRc)
5d: PYRUVIC ACID (PYRd)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
6c: ZINC ION (ZNc)
6d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
4
Ligand/Ion
CHLORIDE ION
2
GOL
2
Ligand/Ion
GLYCEROL
3
KCX
4
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
4
MG
4
Ligand/Ion
MAGNESIUM ION
5
PYR
4
Ligand/Ion
PYRUVIC ACID
6
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(18, 18)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:549 , KCX A:718 , HIS A:747 , HIS A:749 , HOH A:1284
BINDING SITE FOR RESIDUE ZN A 1101
02
AC2
SOFTWARE
TYR A:987 , PRO A:988 , LYS A:989 , VAL A:990
BINDING SITE FOR RESIDUE CL A 1102
03
AC3
SOFTWARE
MET A:534 , ARG A:535 , GLU A:537 , ASP A:768 , HOH A:1206 , HOH A:1260
BINDING SITE FOR RESIDUE MG A 1103
04
AC4
SOFTWARE
ARG A:548 , GLN A:552 , GLY A:586 , LEU A:619 , ARG A:621 , KCX A:718 , VAL A:881 , THR A:882 , HOH A:1284
BINDING SITE FOR RESIDUE PYR A 1104
05
AC5
SOFTWARE
ASP B:750 , GLY B:753 , GLY B:779 , ASN B:780 , ASP D:750 , GLY D:779 , ASN D:780 , HOH D:1221
BINDING SITE FOR RESIDUE GOL B 1101
06
AC6
SOFTWARE
TYR B:987 , PRO B:988 , LYS B:989 , VAL B:990
BINDING SITE FOR RESIDUE CL B 1102
07
AC7
SOFTWARE
MET B:534 , ARG B:535 , GLU B:537 , ASP B:768 , HOH B:1233
BINDING SITE FOR RESIDUE MG B 1103
08
AC8
SOFTWARE
ASP B:549 , KCX B:718 , HIS B:747 , HIS B:749 , HOH B:1246
BINDING SITE FOR RESIDUE ZN B 1104
09
AC9
SOFTWARE
ARG B:548 , GLN B:552 , GLY B:586 , ALA B:587 , LEU B:619 , ARG B:621 , KCX B:718 , VAL B:881 , THR B:882 , HOH B:1246
BINDING SITE FOR RESIDUE PYR B 1105
10
BC1
SOFTWARE
ASP A:750 , GLY A:779 , ASN A:780 , ASP C:750 , GLY C:753 , GLY C:779 , ASN C:780
BINDING SITE FOR RESIDUE GOL C 1101
11
BC2
SOFTWARE
TYR C:987 , PRO C:988 , LYS C:989 , VAL C:990 , HOH C:1234
BINDING SITE FOR RESIDUE CL C 1102
12
BC3
SOFTWARE
MET C:534 , ARG C:535 , GLU C:537 , ASP C:768 , HOH C:1231
BINDING SITE FOR RESIDUE MG C 1103
13
BC4
SOFTWARE
ASP C:549 , KCX C:718 , HIS C:747 , HIS C:749 , HOH C:1242
BINDING SITE FOR RESIDUE ZN C 1104
14
BC5
SOFTWARE
ARG C:548 , GLN C:552 , GLY C:586 , LEU C:619 , ARG C:621 , PHE C:654 , KCX C:718 , THR C:882 , HOH C:1242
BINDING SITE FOR RESIDUE PYR C 1105
15
BC6
SOFTWARE
TYR D:987 , PRO D:988 , LYS D:989 , VAL D:990
BINDING SITE FOR RESIDUE CL D 1101
16
BC7
SOFTWARE
MET D:534 , ARG D:535 , GLU D:537 , ASP D:768 , HOH D:1223
BINDING SITE FOR RESIDUE MG D 1102
17
BC8
SOFTWARE
ASP D:549 , KCX D:718 , HIS D:747 , HIS D:749
BINDING SITE FOR RESIDUE ZN D 1103
18
BC9
SOFTWARE
ARG D:548 , GLN D:552 , GLY D:586 , LEU D:619 , ARG D:621 , KCX D:718 , THR D:882
BINDING SITE FOR RESIDUE PYR D 1104
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (769 KB)
Header - Asym.Unit
Biol.Unit 1 (758 KB)
Header - Biol.Unit 1
Biol.Unit 2 (386 KB)
Header - Biol.Unit 2
Biol.Unit 3 (380 KB)
Header - Biol.Unit 3
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
4JX5
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
