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.
3DTB
Biol. Unit 3
Info
Asym.Unit (244 KB)
Biol.Unit 1 (122 KB)
Biol.Unit 2 (119 KB)
Biol.Unit 3 (235 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH PHOSPHOGLYCOLATE AND GDP
Authors
:
S. M. Sullivan, T. Holyoak
Date
:
14 Jul 08 (Deposition) - 26 Aug 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (1x)
Keywords
:
Kinase, Gluconeogenesis, Lyase, Decarboxylase, Gtp-Binding, Nucleotide-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. M. Sullivan, T. Holyoak
Enzymes With Lid-Gated Active Sites Must Operate By An Induced Fit Mechanism Instead Of Conformational Selection.
Proc. Natl. Acad. Sci. Usa V. 105 13829 2008
[
close entry info
]
Hetero Components
(5, 8)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1b: PENTAETHYLENE GLYCOL (1PEb)
2a: BICARBONATE ION (BCTa)
3a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
4a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
4b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
5a: MANGANESE (II) ION (MNa)
5b: MANGANESE (II) ION (MNb)
5c: MANGANESE (II) ION (MNc)
5d: MANGANESE (II) ION (MNd)
6a: SODIUM ION (NAa)
6b: SODIUM ION (NAb)
7a: 2-PHOSPHOGLYCOLIC ACID (PGAa)
7b: 2-PHOSPHOGLYCOLIC ACID (PGAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
2
Ligand/Ion
PENTAETHYLENE GLYCOL
2
BCT
1
Ligand/Ion
BICARBONATE ION
3
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4
GDP
2
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
5
MN
-1
Ligand/Ion
MANGANESE (II) ION
6
NA
-1
Ligand/Ion
SODIUM ION
7
PGA
2
Ligand/Ion
2-PHOSPHOGLYCOLIC ACID
[
close Hetero Component info
]
Sites
(14, 14)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:87 , LYS A:244 , HIS A:264 , SER A:286 , ALA A:287 , LYS A:290 , ASP A:311 , ARG A:405 , PHE A:485
BINDING SITE FOR RESIDUE PGA A 900
02
AC2
SOFTWARE
ARG B:87 , GLY B:236 , GLY B:237 , LYS B:244 , ASP B:311 , ARG B:405
BINDING SITE FOR RESIDUE PGA B 900
03
AC3
SOFTWARE
LYS A:244 , HIS A:264 , ASP A:311
BINDING SITE FOR RESIDUE MN A 700
04
AC4
SOFTWARE
THR A:291
BINDING SITE FOR RESIDUE MN A 701
05
AC5
SOFTWARE
LEU A:79 , ASN A:208
BINDING SITE FOR RESIDUE NA A 1100
06
AC6
SOFTWARE
LYS B:244 , HIS B:264 , ASP B:311
BINDING SITE FOR RESIDUE MN B 700
07
AC7
SOFTWARE
THR B:291
BINDING SITE FOR RESIDUE MN B 701
08
AC8
SOFTWARE
LEU B:79 , ASN B:208
BINDING SITE FOR RESIDUE NA B 1100
09
AC9
SOFTWARE
ILE A:95 , LEU A:222 , PRO A:223 , ASP A:224 , ARG A:225 , GLY B:570
BINDING SITE FOR RESIDUE BCT A 1044
10
BC1
SOFTWARE
PRO A:285 , ALA A:287 , CYS A:288 , GLY A:289 , LYS A:290 , THR A:291 , ASN A:292 , PRO A:337 , ARG A:436 , TRP A:516 , PHE A:517 , PHE A:525 , GLY A:529 , PHE A:530 , ASN A:533
BINDING SITE FOR RESIDUE GDP A 800
11
BC2
SOFTWARE
LEU A:153 , TRP A:260 , LYS A:316 , ARG A:324 , GLU A:424
BINDING SITE FOR RESIDUE 1PE A 1000
12
BC3
SOFTWARE
PRO B:285 , ALA B:287 , CYS B:288 , GLY B:289 , LYS B:290 , THR B:291 , ASN B:292 , ARG B:436 , TRP B:516 , PHE B:517 , PHE B:525 , GLY B:529 , PHE B:530 , ASN B:533
BINDING SITE FOR RESIDUE GDP B 800
13
BC4
SOFTWARE
ASN A:7 , ASP A:10 , ALA A:13 , LYS A:14 , GLN A:39
BINDING SITE FOR RESIDUE 1PE A 1101
14
BC5
SOFTWARE
PHE A:30 , ASN A:34 , GLU A:123 , PHE A:126 , LYS A:191 , GLU A:227 , ILE A:229
BINDING SITE FOR RESIDUE EPE A 3380
[
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: PEPCK_GTP (A:284-292,B:284-292)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PEPCK_GTP
PS00505
Phosphoenolpyruvate carboxykinase (GTP) signature.
PCKGC_RAT
284-292
2
A:284-292
B:284-292
[
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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3dtba1 (A:3-259)
1b: SCOP_d3dtbb1 (B:3-259)
2a: SCOP_d3dtba2 (A:260-622)
2b: SCOP_d3dtbb2 (B:260-622)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PEP carboxykinase N-terminal domain
(54)
Superfamily
:
PEP carboxykinase N-terminal domain
(54)
Family
:
PEP carboxykinase N-terminal domain
(48)
Protein domain
:
Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)
(32)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(25)
1a
d3dtba1
A:3-259
1b
d3dtbb1
B:3-259
Fold
:
PEP carboxykinase-like
(61)
Superfamily
:
PEP carboxykinase-like
(61)
Family
:
PEP carboxykinase C-terminal domain
(48)
Protein domain
:
Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)
(32)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(25)
2a
d3dtba2
A:260-622
2b
d3dtbb2
B:260-622
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_3dtbA01 (A:11-64,A:88-259)
1b: CATH_3dtbB01 (B:10-64,B:88-259)
2a: CATH_3dtbB03 (B:260-329,B:415-622)
2b: CATH_3dtbA03 (A:260-329,A:415-622)
3a: CATH_3dtbA02 (A:65-87,A:330-414)
3b: CATH_3dtbB02 (B:65-87,B:330-414)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 1
(42)
Homologous Superfamily
:
Phosphoenolpyruvate Carboxykinase, domain 1
(42)
Brown rat,rat,rats (Rattus norvegicus)
(4)
1a
3dtbA01
A:11-64,A:88-259
1b
3dtbB01
B:10-64,B:88-259
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 3
(62)
Homologous Superfamily
:
[code=3.90.228.20, no name defined]
(42)
Brown rat,rat,rats (Rattus norvegicus)
(4)
2a
3dtbB03
B:260-329,B:415-622
2b
3dtbA03
A:260-329,A:415-622
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 2
(42)
Homologous Superfamily
:
Phosphoenolpyruvate Carboxykinase, domain 2
(42)
Brown rat,rat,rats (Rattus norvegicus)
(4)
3a
3dtbA02
A:65-87,A:330-414
3b
3dtbB02
B:65-87,B:330-414
[
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 (244 KB)
Header - Asym.Unit
Biol.Unit 1 (122 KB)
Header - Biol.Unit 1
Biol.Unit 2 (119 KB)
Header - Biol.Unit 2
Biol.Unit 3 (235 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
3DTB
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
