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.
2VJY
Biol. Unit 1
Info
Asym.Unit (379 KB)
Biol.Unit 1 (190 KB)
Biol.Unit 2 (189 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PYRUVATE DECARBOXYLASE FROM KLUYVEROMYCES LACTIS IN COMPLEX WITH THE SUBSTRATE ANALOGUE METHYL ACETYLPHOSPHONATE
Authors
:
S. Kutter, G. Wille, M. S. Weiss, S. Konig
Date
:
14 Dec 07 (Deposition) - 27 Jan 09 (Release) - 05 May 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Metal-Binding, Decarboxylase, Dimer Of Dimers, Methylacetylphosphonate, Methyl Acetylphosphonate, Substrate Activation, Thiamine Diphosphate, Thiamine Pyrophosphate, Asymmetric Active Sites, Map, Lyase, Pyruvate, Magnesium, Flavoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Kutter, M. S. Weiss, G. Wille, R. Golbik, M. Spinka, S. Konig
Covalently Bound Substrate At The Regulatory Site Of Yeast Pyruvate Decarboxylases Triggers Allosteric Enzyme Activation.
J. Biol. Chem. V. 284 12136 2009
[
close entry info
]
Hetero Components
(3, 8)
Info
All Hetero Components
1a: (1R)-1-[DIHYDROXY(METHOXY)-LAMBDA^... (ALKa)
1b: (1R)-1-[DIHYDROXY(METHOXY)-LAMBDA^... (ALKb)
1c: (1R)-1-[DIHYDROXY(METHOXY)-LAMBDA^... (ALKc)
1d: (1R)-1-[DIHYDROXY(METHOXY)-LAMBDA^... (ALKd)
1e: (1R)-1-[DIHYDROXY(METHOXY)-LAMBDA^... (ALKe)
1f: (1R)-1-[DIHYDROXY(METHOXY)-LAMBDA^... (ALKf)
1g: (1R)-1-[DIHYDROXY(METHOXY)-LAMBDA^... (ALKg)
1h: (1R)-1-[DIHYDROXY(METHOXY)-LAMBDA^... (ALKh)
2a: METHYL HYDROGEN (S)-ACETYLPHOSPHON... (ALUa)
2b: METHYL HYDROGEN (S)-ACETYLPHOSPHON... (ALUb)
2c: METHYL HYDROGEN (S)-ACETYLPHOSPHON... (ALUc)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: THIAMINE DIPHOSPHATE (TPPa)
4b: THIAMINE DIPHOSPHATE (TPPb)
4c: THIAMINE DIPHOSPHATE (TPPc)
4d: THIAMINE DIPHOSPHATE (TPPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ALK
4
Ligand/Ion
(1R)-1-[DIHYDROXY(METHOXY)-LAMBDA^5^-PHOSPHANYL]ETHANOL
2
ALU
2
Ligand/Ion
METHYL HYDROGEN (S)-ACETYLPHOSPHONATE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
TPP
2
Ligand/Ion
THIAMINE DIPHOSPHATE
[
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
GLY A:389 , THR A:390 , GLY A:413 , SER A:414 , ILE A:415 , GLY A:443 , ASP A:444 , GLY A:445 , SER A:446 , ASN A:471 , GLY A:473 , TYR A:474 , THR A:475 , ILE A:476 , GLU A:477 , MG A:601 , ALK A:602 , HOH A:2209 , HOH A:2238 , HOH A:2298 , PRO B:26 , GLY B:27 , GLU B:51 , VAL B:76 , HIS B:115
BINDING SITE FOR RESIDUE TPP A 600
02
AC2
SOFTWARE
ASP A:444 , ASN A:471 , GLY A:473 , TPP A:600 , HOH A:2238
BINDING SITE FOR RESIDUE MG A 601
03
AC3
SOFTWARE
PHE A:292 , THR A:388 , GLU A:477 , ILE A:480 , TPP A:600 , GLY B:27 , ASP B:28 , HIS B:114 , HIS B:115 , HOH B:2042
BINDING SITE FOR RESIDUE ALK A 602
04
AC4
SOFTWARE
HIS A:92 , CYS A:221 , HIS A:225 , GLY A:286 , ALA A:287 , HIS A:310 , SER A:311 , HOH A:2299 , HOH A:2300
BINDING SITE FOR RESIDUE ALK A 603
05
AC5
SOFTWARE
GLN A:16 , VAL A:17 , GLU A:18 , LYS A:65 , TYR A:157
BINDING SITE FOR RESIDUE ALU A 604
06
AC6
SOFTWARE
PRO A:26 , GLY A:27 , GLU A:51 , VAL A:76 , HIS A:115 , THR B:390 , GLY B:413 , SER B:414 , ILE B:415 , GLY B:443 , ASP B:444 , GLY B:445 , SER B:446 , ASN B:471 , GLY B:473 , TYR B:474 , THR B:475 , ILE B:476 , GLU B:477 , MG B:601 , ALK B:602 , HOH B:2212 , HOH B:2214 , HOH B:2300
BINDING SITE FOR RESIDUE TPP B 600
07
AC7
SOFTWARE
ASP B:444 , ASN B:471 , GLY B:473 , TPP B:600 , HOH B:2300
BINDING SITE FOR RESIDUE MG B 601
08
AC8
SOFTWARE
GLY A:27 , ASP A:28 , HIS A:114 , HIS A:115 , HOH A:2014 , PHE B:292 , THR B:388 , GLU B:477 , ILE B:480 , TPP B:600
BINDING SITE FOR RESIDUE ALK B 602
09
AC9
SOFTWARE
HIS B:92 , CYS B:221 , HIS B:225 , GLY B:286 , ALA B:287 , HIS B:310 , SER B:311 , HOH B:2161
BINDING SITE FOR RESIDUE ALK B 603
10
BC1
SOFTWARE
VAL B:17 , LYS B:65 , TYR B:157
BINDING SITE FOR RESIDUE ALU B 604
[
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: TPP_ENZYMES (A:427-446,B:427-446)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TPP_ENZYMES
PS00187
Thiamine pyrophosphate enzymes signature.
PDC1_KLULA
427-446
2
A:427-446
B:427-446
-
-
[
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, 12)
Info
All SCOP Domains
1a: SCOP_d2vjya2 (A:182-360)
1b: SCOP_d2vjyb2 (B:182-360)
1c: SCOP_d2vjyc2 (C:182-360)
1d: SCOP_d2vjyd2 (D:182-360)
2a: SCOP_d2vjya1 (A:2-181)
2b: SCOP_d2vjyb1 (B:2-181)
2c: SCOP_d2vjyb3 (B:361-563)
2d: SCOP_d2vjyc1 (C:2-181)
2e: SCOP_d2vjyc3 (C:361-563)
2f: SCOP_d2vjyd1 (D:2-181)
2g: SCOP_d2vjyd3 (D:361-563)
2h: SCOP_d2vjya3 (A:361-563)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
DHS-like NAD/FAD-binding domain
(176)
Superfamily
:
DHS-like NAD/FAD-binding domain
(176)
Family
:
automated matches
(36)
Protein domain
:
automated matches
(36)
Milk yeast (Kluyveromyces lactis) [TaxId: 28985]
(2)
1a
d2vjya2
A:182-360
1b
d2vjyb2
B:182-360
1c
d2vjyc2
C:182-360
1d
d2vjyd2
D:182-360
Fold
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Superfamily
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Family
:
automated matches
(65)
Protein domain
:
automated matches
(65)
Milk yeast (Kluyveromyces lactis) [TaxId: 28985]
(2)
2a
d2vjya1
A:2-181
2b
d2vjyb1
B:2-181
2c
d2vjyb3
B:361-563
2d
d2vjyc1
C:2-181
2e
d2vjyc3
C:361-563
2f
d2vjyd1
D:2-181
2g
d2vjyd3
D:361-563
2h
d2vjya3
A:361-563
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2vjyA03 (A:353-554)
1b: CATH_2vjyD03 (D:353-554)
1c: CATH_2vjyB03 (B:353-553)
1d: CATH_2vjyC03 (C:353-553)
1e: CATH_2vjyA01 (A:2-188)
1f: CATH_2vjyB01 (B:2-188)
1g: CATH_2vjyC01 (C:2-188)
1h: CATH_2vjyD01 (D:2-188)
2a: CATH_2vjyA02 (A:189-352)
2b: CATH_2vjyB02 (B:189-352)
2c: CATH_2vjyC02 (C:189-352)
2d: CATH_2vjyD02 (D:189-352)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Yeast (Kluyveromyces lactis)
(1)
1a
2vjyA03
A:353-554
1b
2vjyD03
D:353-554
1c
2vjyB03
B:353-553
1d
2vjyC03
C:353-553
1e
2vjyA01
A:2-188
1f
2vjyB01
B:2-188
1g
2vjyC01
C:2-188
1h
2vjyD01
D:2-188
Homologous Superfamily
:
TPP-binding domain
(120)
Yeast (Kluyveromyces lactis)
(1)
2a
2vjyA02
A:189-352
2b
2vjyB02
B:189-352
2c
2vjyC02
C:189-352
2d
2vjyD02
D:189-352
[
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 (379 KB)
Header - Asym.Unit
Biol.Unit 1 (190 KB)
Header - Biol.Unit 1
Biol.Unit 2 (189 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
2VJY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help