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.
1A3X
Biol. Unit 2
Info
Asym.Unit (146 KB)
Biol.Unit 1 (277 KB)
Biol.Unit 2 (140 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PYRUVATE KINASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH PG, MN2+ AND K+
Authors
:
M. S. Jurica, A. Mesecar, P. J. Heath, W. Shi, T. Nowak, B. L. Stoddard
Date
:
26 Jan 98 (Deposition) - 27 May 98 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Biol. Unit 2: A,B (1x)
Keywords
:
Pyruvate Kinase, Allosteric Regulation, Tranferase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. S. Jurica, A. Mesecar, P. J. Heath, W. Shi, T. Nowak, B. L. Stoddard
The Allosteric Regulation Of Pyruvate Kinase By Fructose-1, 6-Bisphosphate.
Structure V. 6 195 1998
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
3a: 2-PHOSPHOGLYCOLIC ACID (PGAa)
3b: 2-PHOSPHOGLYCOLIC ACID (PGAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
-1
Ligand/Ion
POTASSIUM ION
2
MN
-1
Ligand/Ion
MANGANESE (II) ION
3
PGA
1
Ligand/Ion
2-PHOSPHOGLYCOLIC ACID
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:49 , LYS A:240 , GLU A:242 , ALA A:263 , ARG A:264 , GLY A:265 , ASP A:266 , THR A:298 , MN A:1001 , K A:1002
BINDING SITE FOR RESIDUE PGA A 1005
2
AC2
SOFTWARE
ARG B:49 , SER B:213 , LYS B:240 , GLU B:242 , ALA B:263 , ARG B:264 , GLY B:265 , ASP B:266 , ALA B:297 , THR B:298 , MN B:1003 , K B:1004
BINDING SITE FOR RESIDUE PGA B 1006
3
AC3
SOFTWARE
GLU A:242 , ASP A:266 , PGA A:1005
BINDING SITE FOR RESIDUE MN A 1001
4
AC4
SOFTWARE
ASN A:51 , SER A:53 , ASP A:84 , THR A:85 , SER A:213 , LYS A:240 , PGA A:1005
BINDING SITE FOR RESIDUE K A 1002
5
AC5
SOFTWARE
GLU B:242 , ASP B:266 , PGA B:1006
BINDING SITE FOR RESIDUE MN B 1003
6
AC6
SOFTWARE
ASN B:51 , SER B:53 , ASP B:84 , THR B:85 , SER B:213 , PGA B:1006
BINDING SITE FOR RESIDUE K B 1004
[
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: PYRUVATE_KINASE (A:235-247,B:235-247)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PYRUVATE_KINASE
PS00110
Pyruvate kinase active site signature.
KPYK1_YEAST
235-247
2
A:235-247
B:235-247
[
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, 6)
Info
All SCOP Domains
1a: SCOP_d1a3xa1 (A:88-188)
1b: SCOP_d1a3xb1 (B:88-188)
2a: SCOP_d1a3xa3 (A:367-500)
2b: SCOP_d1a3xb3 (B:367-500)
3a: SCOP_d1a3xa2 (A:1-87,A:189-366)
3b: SCOP_d1a3xb2 (B:1-87,B:189-366)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
PK beta-barrel domain-like
(31)
Superfamily
:
PK beta-barrel domain-like
(31)
Family
:
Pyruvate kinase beta-barrel domain
(28)
Protein domain
:
Pyruvate kinase (PK)
(28)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(2)
1a
d1a3xa1
A:88-188
1b
d1a3xb1
B:88-188
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Pyruvate kinase C-terminal domain-like
(59)
Superfamily
:
PK C-terminal domain-like
(30)
Family
:
Pyruvate kinase, C-terminal domain
(28)
Protein domain
:
Pyruvate kinase, C-terminal domain
(28)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(2)
2a
d1a3xa3
A:367-500
2b
d1a3xb3
B:367-500
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Phosphoenolpyruvate/pyruvate domain
(92)
Family
:
Pyruvate kinase
(28)
Protein domain
:
Pyruvate kinase, N-terminal domain
(28)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(2)
3a
d1a3xa2
A:1-87,A:189-366
3b
d1a3xb2
B:1-87,B:189-366
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1a3xA01 (A:1-18,A:356-500)
1b: CATH_1a3xB01 (B:1-18,B:356-498)
2a: CATH_1a3xA02 (A:19-87,A:190-355)
2b: CATH_1a3xB02 (B:19-87,B:190-355)
3a: CATH_1a3xA03 (A:88-189)
3b: CATH_1a3xB03 (B:88-189)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Pyruvate Kinase; Chain: A, domain 1
(36)
Homologous Superfamily
:
[code=3.40.1380.20, no name defined]
(20)
Baker's yeast (Saccharomyces cerevisiae)
(2)
1a
1a3xA01
A:1-18,A:356-500
1b
1a3xB01
B:1-18,B:356-498
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Phosphoenolpyruvate-binding domains
(67)
Baker's yeast (Saccharomyces cerevisiae)
(2)
2a
1a3xA02
A:19-87,A:190-355
2b
1a3xB02
B:19-87,B:190-355
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
M1 Pyruvate Kinase; Domain 3
(24)
Homologous Superfamily
:
M1 Pyruvate Kinase; Domain 3
(20)
Baker's yeast (Saccharomyces cerevisiae)
(2)
3a
1a3xA03
A:88-189
3b
1a3xB03
B:88-189
[
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
Asymmetric Unit 2
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 (146 KB)
Header - Asym.Unit
Biol.Unit 1 (277 KB)
Header - Biol.Unit 1
Biol.Unit 2 (140 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
1A3X
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help