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.
1W85
Biol. Unit 2
Info
Asym.Unit (475 KB)
Biol.Unit 1 (240 KB)
Biol.Unit 2 (234 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE CRYSTAL STRUCTURE OF PYRUVATE DEHYDROGENASE E1 BOUND TO THE PERIPHERAL SUBUNIT BINDING DOMAIN OF E2
Authors
:
R. A. W. Frank, J. V. Pratap, X. Y. Pei, R. N. Perham, B. F. Luisi
Date
:
16 Sep 04 (Deposition) - 02 Nov 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,I (1x)
Biol. Unit 2: E,F,G,H,J (1x)
Keywords
:
Pyruvate, Dehydrogenase, Dihydrolipoyl, Acetyl Transferase, Multienzyme Complex, Oxidoreductase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. A. W. Frank, C. M. Titman, J. V. Pratap, B. F. Luisi, R. N. Perham
A Molecular Switch And Proton Wire Synchronize The Active Sites In Thiamine Enzymes
Science V. 306 872 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 3)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
3a: DI(HYDROXYETHYL)ETHER (PEGa)
3b: DI(HYDROXYETHYL)ETHER (PEGb)
3c: DI(HYDROXYETHYL)ETHER (PEGc)
4a: THIAMIN DIPHOSPHATE (TDPa)
4b: THIAMIN DIPHOSPHATE (TDPb)
4c: THIAMIN DIPHOSPHATE (TDPc)
4d: THIAMIN DIPHOSPHATE (TDPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
-1
Ligand/Ion
POTASSIUM ION
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
4
TDP
2
Ligand/Ion
THIAMIN DIPHOSPHATE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC6 (SOFTWARE)
2: AC7 (SOFTWARE)
3: AC8 (SOFTWARE)
4: AC9 (SOFTWARE)
5: BC1 (SOFTWARE)
6: BC4 (SOFTWARE)
7: BC5 (SOFTWARE)
8: BC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC6
SOFTWARE
ASP E:173 , ASN E:202 , TDP E:1370 , HOH E:2079 , HOH E:2087
BINDING SITE FOR RESIDUE MG E1368
2
AC7
SOFTWARE
ILE F:112 , THR F:113 , ALA F:160 , ASP F:163 , ASP F:165 , HOH F:2060
BINDING SITE FOR RESIDUE K F1325
3
AC8
SOFTWARE
HOH E:2083 , HOH E:2084 , HOH F:2045 , HOH G:2125 , HOH G:2127 , HOH H:2057
BINDING SITE FOR RESIDUE MG F1326
4
AC9
SOFTWARE
ASP G:173 , ASN G:202 , PHE G:204 , TDP G:1370 , HOH G:2131
BINDING SITE FOR RESIDUE MG G1368
5
BC1
SOFTWARE
ILE H:112 , THR H:113 , ALA H:160 , ASP H:163 , ASP H:165 , HOH H:2072
BINDING SITE FOR RESIDUE K H1325
6
BC4
SOFTWARE
TYR E:102 , ARG E:103 , ILE E:142 , ILE E:144 , GLY E:172 , ASP E:173 , GLY E:174 , GLY E:175 , GLN E:178 , ASN E:202 , HIS E:271 , MG E:1368 , HOH E:2087 , HOH E:2136 , HOH E:2137 , GLU H:28 , LEU H:57 , GLU H:59 , GLN H:81 , PHE H:85
BINDING SITE FOR RESIDUE TDP E1370
7
BC5
SOFTWARE
GLU F:28 , LEU F:57 , GLU F:59 , GLN F:81 , PHE F:85 , TYR G:102 , ARG G:103 , ILE G:142 , ILE G:144 , GLY G:172 , ASP G:173 , GLY G:174 , GLY G:175 , GLN G:178 , ASN G:202 , PHE G:204 , ALA G:205 , ILE G:206 , HIS G:271 , MG G:1368 , HOH G:2131 , HOH G:2231 , HOH G:2232 , HOH G:2233 , HOH G:2234
BINDING SITE FOR RESIDUE TDP G1370
8
BC8
SOFTWARE
ILE G:109 , TRP G:110 , GLU G:324
BINDING SITE FOR RESIDUE PEG G1369
[
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, 1)
Info
All PROSITE Patterns/Profiles
1: PSBD (J:130-167)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PSBD
PS51826
Peripheral subunit-binding (PSBD) domain profile.
ODP2_GEOSE
130-167
1
-
J:130-167
[
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
(4, 14)
Info
All SCOP Domains
1a: SCOP_d1w85i_ (I:)
1b: SCOP_d1w85j_ (J:)
2a: SCOP_d1w85a_ (A:)
2b: SCOP_d1w85c_ (C:)
2c: SCOP_d1w85e_ (E:)
2d: SCOP_d1w85g_ (G:)
3a: SCOP_d1w85b1 (B:1-192)
3b: SCOP_d1w85d1 (D:1-192)
3c: SCOP_d1w85f1 (F:1-192)
3d: SCOP_d1w85h1 (H:1-192)
4a: SCOP_d1w85b2 (B:193-324)
4b: SCOP_d1w85d2 (D:193-324)
4c: SCOP_d1w85f2 (F:193-324)
4d: SCOP_d1w85h2 (H:193-324)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
(21)
Superfamily
:
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
(21)
Family
:
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
(16)
Protein domain
:
E3/E1 binding domain of dihydrolipoyl acetyltransferase
(5)
Bacillus stearothermophilus [TaxId: 1422]
(5)
1a
d1w85i_
I:
1b
d1w85j_
J:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Superfamily
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Family
:
Branched-chain alpha-keto acid dehydrogenase PP module
(42)
Protein domain
:
Pyruvate dehydrogenase E1-alpha, PdhA
(2)
Bacillus stearothermophilus [TaxId: 1422]
(2)
2a
d1w85a_
A:
2b
d1w85c_
C:
2c
d1w85e_
E:
2d
d1w85g_
G:
Family
:
Branched-chain alpha-keto acid dehydrogenase Pyr module
(36)
Protein domain
:
Pyruvate dehydrogenase E1-beta, PdhB, N-terminal domain
(2)
Bacillus stearothermophilus [TaxId: 1422]
(2)
3a
d1w85b1
B:1-192
3b
d1w85d1
D:1-192
3c
d1w85f1
F:1-192
3d
d1w85h1
H:1-192
Fold
:
TK C-terminal domain-like
(79)
Superfamily
:
TK C-terminal domain-like
(79)
Family
:
Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain
(39)
Protein domain
:
Pyruvate dehydrogenase E1-beta, PdhB, C-terminal domain
(2)
Bacillus stearothermophilus [TaxId: 1422]
(2)
4a
d1w85b2
B:193-324
4b
d1w85d2
D:193-324
4c
d1w85f2
F:193-324
4d
d1w85h2
H:193-324
[
close SCOP info
]
CATH Domains
(3, 13)
Info
all CATH domains
1a: CATH_1w85B02 (B:192-324)
1b: CATH_1w85D02 (D:192-324)
1c: CATH_1w85F02 (F:192-324)
1d: CATH_1w85H02 (H:192-324)
2a: CATH_1w85B01 (B:1-191)
2b: CATH_1w85D01 (D:1-191)
2c: CATH_1w85E00 (E:5-368)
2d: CATH_1w85A00 (A:4-368)
2e: CATH_1w85G00 (G:5-368)
2f: CATH_1w85C00 (C:4-368)
2g: CATH_1w85F01 (F:1-191)
2h: CATH_1w85H01 (H:1-191)
3a: CATH_1w85I00 (I:128-169)
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=3.40.50.920, no name defined]
(73)
Geobacillus stearothermophilus. Organism_taxid: 1422.
(2)
1a
1w85B02
B:192-324
1b
1w85D02
D:192-324
1c
1w85F02
F:192-324
1d
1w85H02
H:192-324
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Geobacillus stearothermophilus. Organism_taxid: 1422.
(2)
2a
1w85B01
B:1-191
2b
1w85D01
D:1-191
2c
1w85E00
E:5-368
2d
1w85A00
A:4-368
2e
1w85G00
G:5-368
2f
1w85C00
C:4-368
2g
1w85F01
F:1-191
2h
1w85H01
H:1-191
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Dihydrolipoamide Transferase
(20)
Homologous Superfamily
:
Dihydrolipoamide Transferase
(20)
Geobacillus stearothermophilus. Organism_taxid: 1422.
(4)
3a
1w85I00
I:128-169
[
close CATH info
]
Pfam Domains
(4, 14)
Info
all PFAM domains
1a: PFAM_E1_dh_1w85G01 (G:50-341)
1b: PFAM_E1_dh_1w85G02 (G:50-341)
1c: PFAM_E1_dh_1w85G03 (G:50-341)
1d: PFAM_E1_dh_1w85G04 (G:50-341)
2a: PFAM_Transket_pyr_1w85H01 (H:1-179)
2b: PFAM_Transket_pyr_1w85H02 (H:1-179)
2c: PFAM_Transket_pyr_1w85H03 (H:1-179)
2d: PFAM_Transket_pyr_1w85H04 (H:1-179)
3a: PFAM_E3_binding_1w85J01 (J:129-165)
3b: PFAM_E3_binding_1w85J02 (J:129-165)
4a: PFAM_Transketolase_C_1w85H05 (H:193-315)
4b: PFAM_Transketolase_C_1w85H06 (H:193-315)
4c: PFAM_Transketolase_C_1w85H07 (H:193-315)
4d: PFAM_Transketolase_C_1w85H08 (H:193-315)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
THDP-binding
(106)
Family
:
E1_dh
(27)
Geobacillus stearothermophilus (Bacillus stearothermophilus)
(2)
1a
E1_dh-1w85G01
G:50-341
1b
E1_dh-1w85G02
G:50-341
1c
E1_dh-1w85G03
G:50-341
1d
E1_dh-1w85G04
G:50-341
Family
:
Transket_pyr
(45)
Geobacillus stearothermophilus (Bacillus stearothermophilus)
(2)
2a
Transket_pyr-1w85H01
H:1-179
2b
Transket_pyr-1w85H02
H:1-179
2c
Transket_pyr-1w85H03
H:1-179
2d
Transket_pyr-1w85H04
H:1-179
Clan
:
no clan defined [family: E3_binding]
(14)
Family
:
E3_binding
(14)
Geobacillus stearothermophilus (Bacillus stearothermophilus)
(7)
3a
E3_binding-1w85J01
J:129-165
3b
E3_binding-1w85J02
J:129-165
Clan
:
no clan defined [family: Transketolase_C]
(40)
Family
:
Transketolase_C
(40)
Geobacillus stearothermophilus (Bacillus stearothermophilus)
(2)
4a
Transketolase_C-1w85H05
H:193-315
4b
Transketolase_C-1w85H06
H:193-315
4c
Transketolase_C-1w85H07
H:193-315
4d
Transketolase_C-1w85H08
H:193-315
[
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 E
Chain F
Chain G
Chain H
Chain J
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 (475 KB)
Header - Asym.Unit
Biol.Unit 1 (240 KB)
Header - Biol.Unit 1
Biol.Unit 2 (234 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
1W85
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help