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.
1ZPD
Asym. Unit
Info
Asym.Unit (399 KB)
Biol.Unit 1 (393 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 ZYMOMONAS MOBILIS
Authors
:
G. Lu, D. Dobritzsch, G. Schneider
Date
:
17 Apr 98 (Deposition) - 02 Feb 99 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.86
Chains
:
Asym. Unit : A,B,E,F
Biol. Unit 1: A,B,E,F (1x)
Keywords
:
Alcohol Fermentation, Thiamin Diphosphate, Decarboxylase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Dobritzsch, S. Konig, G. Schneider, G. Lu
High Resolution Crystal Structure Of Pyruvate Decarboxylase From Zymomonas Mobilis. Implications For Substrate Activation In Pyruvate Decarboxylases.
J. Biol. Chem. V. 273 20196 1998
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 12)
Info
All Hetero Components
1a: CITRIC ACID (CITa)
1b: CITRIC ACID (CITb)
1c: CITRIC ACID (CITc)
1d: CITRIC ACID (CITd)
2a: MONO-{4-[(4-AMINO-2-METHYL-PYRIMID... (DPXa)
2b: MONO-{4-[(4-AMINO-2-METHYL-PYRIMID... (DPXb)
2c: MONO-{4-[(4-AMINO-2-METHYL-PYRIMID... (DPXc)
2d: MONO-{4-[(4-AMINO-2-METHYL-PYRIMID... (DPXd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CIT
4
Ligand/Ion
CITRIC ACID
2
DPX
4
Ligand/Ion
MONO-{4-[(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-AMINO]-2-HYDROXY-3-MERCAPTO-PENT-3-ENYL-PHOSPHONO}ESTER
3
MG
4
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:440 , ASN A:467 , GLY A:469 , DPX A:600 , HOH A:611
BINDING SITE FOR RESIDUE MG A 601
02
AC2
SOFTWARE
ASP B:440 , ASN B:467 , GLY B:469 , DPX B:600 , HOH B:611
BINDING SITE FOR RESIDUE MG B 601
03
AC3
SOFTWARE
ASP E:440 , ASN E:467 , GLY E:469 , DPX E:600 , HOH E:611
BINDING SITE FOR RESIDUE MG E 601
04
AC4
SOFTWARE
ASP F:440 , ASN F:467 , GLY F:469 , DPX F:600 , HOH F:611
BINDING SITE FOR RESIDUE MG F 601
05
AC5
SOFTWARE
ASP A:390 , GLY A:413 , HIS A:414 , ILE A:415 , GLY A:439 , ASP A:440 , GLY A:441 , SER A:442 , ASN A:467 , GLY A:469 , TYR A:470 , THR A:471 , ILE A:472 , GLU A:473 , MG A:601 , HOH A:611 , HOH A:612 , HOH A:769 , HOH A:1256 , ALA B:25 , GLY B:26 , GLU B:50 , VAL B:75 , HIS B:114
BINDING SITE FOR RESIDUE DPX A 600
06
AC6
SOFTWARE
ARG A:310 , ARG A:318 , PRO A:320 , SER A:321 , HOH A:709 , HOH A:746 , HOH A:789 , HOH A:1006 , HOH A:1049 , HIS F:150 , LYS F:153 , ARG F:157
BINDING SITE FOR RESIDUE CIT A 610
07
AC7
SOFTWARE
ALA A:25 , GLY A:26 , GLU A:50 , VAL A:75 , HIS A:114 , ASP B:390 , GLY B:413 , HIS B:414 , ILE B:415 , GLY B:439 , ASP B:440 , GLY B:441 , SER B:442 , ASN B:467 , GLY B:469 , TYR B:470 , THR B:471 , ILE B:472 , GLU B:473 , MG B:601 , HOH B:611 , HOH B:612 , HOH B:842
BINDING SITE FOR RESIDUE DPX B 600
08
AC8
SOFTWARE
ARG B:310 , ARG B:318 , PRO B:320 , SER B:321 , HOH B:688 , HOH B:782 , HOH B:819 , HOH B:861 , HOH B:1111 , HIS E:150 , LYS E:153 , ARG E:157
BINDING SITE FOR RESIDUE CIT B 610
09
AC9
SOFTWARE
ASP E:390 , GLY E:413 , HIS E:414 , ILE E:415 , GLY E:439 , ASP E:440 , GLY E:441 , SER E:442 , ASN E:467 , GLY E:469 , TYR E:470 , THR E:471 , ILE E:472 , GLU E:473 , MG E:601 , HOH E:611 , HOH E:612 , HOH E:874 , ALA F:25 , GLY F:26 , GLU F:50 , VAL F:75 , HIS F:114
BINDING SITE FOR RESIDUE DPX E 600
10
BC1
SOFTWARE
HIS B:150 , LYS B:153 , ARG B:157 , ARG E:310 , ARG E:318 , PRO E:320 , SER E:321 , HOH E:656 , HOH E:814 , HOH E:851 , HOH E:894 , HOH E:1113
BINDING SITE FOR RESIDUE CIT E 610
11
BC2
SOFTWARE
ALA E:25 , GLY E:26 , GLU E:50 , VAL E:75 , HIS E:114 , ASP F:390 , GLY F:413 , HIS F:414 , ILE F:415 , GLY F:439 , ASP F:440 , GLY F:441 , SER F:442 , ASN F:467 , GLY F:469 , TYR F:470 , THR F:471 , ILE F:472 , GLU F:473 , MG F:601 , HOH F:611 , HOH F:612 , HOH F:943 , HOH F:1240
BINDING SITE FOR RESIDUE DPX F 600
12
BC3
SOFTWARE
HIS A:150 , LYS A:153 , ARG A:157 , ARG F:310 , ARG F:318 , PRO F:320 , SER F:321 , HOH F:712 , HOH F:793 , HOH F:885 , HOH F:920 , HOH F:962
BINDING SITE FOR RESIDUE CIT F 610
[
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
(1, 4)
Info
All PROSITE Patterns/Profiles
1: TPP_ENZYMES (A:423-442,B:423-442,E:423-442,F:42...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TPP_ENZYMES
PS00187
Thiamine pyrophosphate enzymes signature.
PDC_ZYMMO
423-442
4
A:423-442
B:423-442
E:423-442
F:423-442
[
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
(3, 12)
Info
All SCOP Domains
1a: SCOP_d1zpda1 (A:188-362)
1b: SCOP_d1zpdb1 (B:188-362)
1c: SCOP_d1zpde1 (E:188-362)
1d: SCOP_d1zpdf1 (F:188-362)
2a: SCOP_d1zpda3 (A:363-566)
2b: SCOP_d1zpdb3 (B:363-566)
2c: SCOP_d1zpde3 (E:363-566)
2d: SCOP_d1zpdf3 (F:363-566)
3a: SCOP_d1zpda2 (A:2-187)
3b: SCOP_d1zpdb2 (B:2-187)
3c: SCOP_d1zpde2 (E:2-187)
3d: SCOP_d1zpdf2 (F:2-187)
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
:
Pyruvate oxidase and decarboxylase, middle domain
(74)
Protein domain
:
Pyruvate decarboxylase
(4)
Zymomonas mobilis [TaxId: 542]
(1)
1a
d1zpda1
A:188-362
1b
d1zpdb1
B:188-362
1c
d1zpde1
E:188-362
1d
d1zpdf1
F:188-362
Fold
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Superfamily
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Family
:
Pyruvate oxidase and decarboxylase PP module
(43)
Protein domain
:
Pyruvate decarboxylase
(4)
Zymomonas mobilis [TaxId: 542]
(1)
2a
d1zpda3
A:363-566
2b
d1zpdb3
B:363-566
2c
d1zpde3
E:363-566
2d
d1zpdf3
F:363-566
Family
:
Pyruvate oxidase and decarboxylase Pyr module
(43)
Protein domain
:
Pyruvate decarboxylase
(4)
Zymomonas mobilis [TaxId: 542]
(1)
3a
d1zpda2
A:2-187
3b
d1zpdb2
B:2-187
3c
d1zpde2
E:2-187
3d
d1zpdf2
F:2-187
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1zpdA03 (A:355-548)
1b: CATH_1zpdB03 (B:355-548)
1c: CATH_1zpdE03 (E:355-548)
1d: CATH_1zpdF03 (F:355-548)
1e: CATH_1zpdA01 (A:2-186)
1f: CATH_1zpdB01 (B:2-186)
1g: CATH_1zpdE01 (E:2-186)
1h: CATH_1zpdF01 (F:2-186)
2a: CATH_1zpdA02 (A:188-350)
2b: CATH_1zpdB02 (B:188-350)
2c: CATH_1zpdE02 (E:188-350)
2d: CATH_1zpdF02 (F:188-350)
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)
Zymomonas mobilis. Organism_taxid: 542.
(4)
1a
1zpdA03
A:355-548
1b
1zpdB03
B:355-548
1c
1zpdE03
E:355-548
1d
1zpdF03
F:355-548
1e
1zpdA01
A:2-186
1f
1zpdB01
B:2-186
1g
1zpdE01
E:2-186
1h
1zpdF01
F:2-186
Homologous Superfamily
:
TPP-binding domain
(120)
Zymomonas mobilis. Organism_taxid: 542.
(4)
2a
1zpdA02
A:188-350
2b
1zpdB02
B:188-350
2c
1zpdE02
E:188-350
2d
1zpdF02
F:188-350
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_TPP_enzyme_M_1zpdF01 (F:199-360)
1b: PFAM_TPP_enzyme_M_1zpdF02 (F:199-360)
1c: PFAM_TPP_enzyme_M_1zpdF03 (F:199-360)
1d: PFAM_TPP_enzyme_M_1zpdF04 (F:199-360)
2a: PFAM_TPP_enzyme_C_1zpdF05 (F:387-537)
2b: PFAM_TPP_enzyme_C_1zpdF06 (F:387-537)
2c: PFAM_TPP_enzyme_C_1zpdF07 (F:387-537)
2d: PFAM_TPP_enzyme_C_1zpdF08 (F:387-537)
3a: PFAM_TPP_enzyme_N_1zpdF09 (F:3-179)
3b: PFAM_TPP_enzyme_N_1zpdF10 (F:3-179)
3c: PFAM_TPP_enzyme_N_1zpdF11 (F:3-179)
3d: PFAM_TPP_enzyme_N_1zpdF12 (F:3-179)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
FAD_DHS
(82)
Family
:
TPP_enzyme_M
(50)
Zymomonas mobilis
(5)
1a
TPP_enzyme_M-1zpdF01
F:199-360
1b
TPP_enzyme_M-1zpdF02
F:199-360
1c
TPP_enzyme_M-1zpdF03
F:199-360
1d
TPP_enzyme_M-1zpdF04
F:199-360
Clan
:
THDP-binding
(106)
Family
:
TPP_enzyme_C
(54)
Zymomonas mobilis
(5)
2a
TPP_enzyme_C-1zpdF05
F:387-537
2b
TPP_enzyme_C-1zpdF06
F:387-537
2c
TPP_enzyme_C-1zpdF07
F:387-537
2d
TPP_enzyme_C-1zpdF08
F:387-537
Family
:
TPP_enzyme_N
(54)
Zymomonas mobilis
(5)
3a
TPP_enzyme_N-1zpdF09
F:3-179
3b
TPP_enzyme_N-1zpdF10
F:3-179
3c
TPP_enzyme_N-1zpdF11
F:3-179
3d
TPP_enzyme_N-1zpdF12
F:3-179
[
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 E
Chain F
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 (399 KB)
Header - Asym.Unit
Biol.Unit 1 (393 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
1ZPD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help