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.
1UMD
Asym. Unit
Info
Asym.Unit (247 KB)
Biol.Unit 1 (242 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
BRANCHED-CHAIN 2-OXO ACID DEHYDROGENASE (E1) FROM THERMUS THERMOPHILUS HB8 WITH 4-METHYL-2-OXOPENTANOATE AS AN INTERMEDIATE
Authors
:
T. Nakai, N. Nakagawa, N. Maoka, R. Masui, S. Kuramitsu, N. Kamiya, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
25 Sep 03 (Deposition) - 30 Mar 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Alpha(2)Beta(2) Tetramer, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Nakai, N. Nakagawa, N. Maoka, R. Masui, S. Kuramitsu, N. Kamiya
Ligand-Induced Conformational Changes And A Reaction Intermediate In Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus Thermophilus Hb8, As Revealed By X-Ray Crystallography
J. Mol. Biol. V. 337 1011 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 6)
Info
All Hetero Components
1a: 2-OXO-4-METHYLPENTANOIC ACID (COIa)
1b: 2-OXO-4-METHYLPENTANOIC ACID (COIb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: THIAMIN DIPHOSPHATE (TDPa)
3b: THIAMIN DIPHOSPHATE (TDPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
COI
2
Ligand/Ion
2-OXO-4-METHYLPENTANOIC ACID
2
MG
2
Ligand/Ion
MAGNESIUM ION
3
TDP
2
Ligand/Ion
THIAMIN DIPHOSPHATE
[
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
ASP A:175 , ASN A:204 , TYR A:206 , TDP A:1402 , HOH A:1435
BINDING SITE FOR RESIDUE MG A 1401
2
AC2
SOFTWARE
ASP C:175 , ASN C:204 , TYR C:206 , TDP C:2402 , HOH C:2425
BINDING SITE FOR RESIDUE MG C 2401
3
AC3
SOFTWARE
TYR A:94 , TYR A:95 , ARG A:96 , SER A:144 , PRO A:145 , ILE A:146 , GLY A:174 , ASP A:175 , GLY A:176 , ALA A:177 , GLU A:180 , ASN A:204 , TYR A:206 , ALA A:207 , ILE A:208 , HIS A:273 , MG A:1401 , COI A:1403 , HOH A:1413 , HOH A:1434 , HOH A:1435 , GLU D:29 , LEU D:58 , GLU D:60 , GLN D:82 , TYR D:86
BINDING SITE FOR RESIDUE TDP A 1402
4
AC4
SOFTWARE
PHE A:66 , SER A:144 , TDP A:1402 , TYR D:86 , HIS D:129
BINDING SITE FOR RESIDUE COI A 1403
5
AC5
SOFTWARE
GLU B:29 , LEU B:58 , GLU B:60 , GLN B:82 , TYR B:86 , TYR C:94 , TYR C:95 , ARG C:96 , SER C:144 , PRO C:145 , ILE C:146 , GLY C:174 , ASP C:175 , GLY C:176 , ALA C:177 , GLU C:180 , ASN C:204 , TYR C:206 , ALA C:207 , ILE C:208 , HIS C:273 , MG C:2401 , COI C:2403 , HOH C:2422 , HOH C:2425 , HOH C:2439
BINDING SITE FOR RESIDUE TDP C 2402
6
AC6
SOFTWARE
TYR B:86 , HIS B:129 , PHE C:66 , SER C:144 , TDP C:2402
BINDING SITE FOR RESIDUE COI C 2403
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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, 6)
Info
All SCOP Domains
1a: SCOP_d1umda_ (A:)
1b: SCOP_d1umdc_ (C:)
2a: SCOP_d1umdb1 (B:2-187)
2b: SCOP_d1umdd1 (D:2-187)
3a: SCOP_d1umdb2 (B:188-324)
3b: SCOP_d1umdd2 (D:188-324)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
:
Branched-chain alpha-keto acid dehydrogenase, PP module
(23)
Thermus thermophilus [TaxId: 274]
(4)
1a
d1umda_
A:
1b
d1umdc_
C:
Family
:
Branched-chain alpha-keto acid dehydrogenase Pyr module
(36)
Protein domain
:
Branched-chain alpha-keto acid dehydrogenase, Pyr module
(27)
Thermus thermophilus [TaxId: 274]
(4)
2a
d1umdb1
B:2-187
2b
d1umdd1
D:2-187
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
:
Branched-chain alpha-keto acid dehydrogenase
(27)
Thermus thermophilus [TaxId: 274]
(4)
3a
d1umdb2
B:188-324
3b
d1umdd2
D:188-324
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1umdB02 (B:197-324)
1b: CATH_1umdD02 (D:197-324)
2a: CATH_1umdB01 (B:2-196)
2b: CATH_1umdD01 (D:2-196)
2c: CATH_1umdC00 (C:6-366)
2d: CATH_1umdA00 (A:6-367)
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)
Thermus thermophilus. Organism_taxid: 274.
(4)
1a
1umdB02
B:197-324
1b
1umdD02
D:197-324
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Thermus thermophilus. Organism_taxid: 274.
(4)
2a
1umdB01
B:2-196
2b
1umdD01
D:2-196
2c
1umdC00
C:6-366
2d
1umdA00
A:6-367
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_E1_dh_1umdC01 (C:42-342)
1b: PFAM_E1_dh_1umdC02 (C:42-342)
2a: PFAM_Transket_pyr_1umdD01 (D:2-180)
2b: PFAM_Transket_pyr_1umdD02 (D:2-180)
3a: PFAM_Transketolase_C_1umdD03 (D:194-314)
3b: PFAM_Transketolase_C_1umdD04 (D:194-314)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
THDP-binding
(106)
Family
:
E1_dh
(27)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(4)
1a
E1_dh-1umdC01
C:42-342
1b
E1_dh-1umdC02
C:42-342
Family
:
Transket_pyr
(45)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(4)
2a
Transket_pyr-1umdD01
D:2-180
2b
Transket_pyr-1umdD02
D:2-180
Clan
:
no clan defined [family: Transketolase_C]
(40)
Family
:
Transketolase_C
(40)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(4)
3a
Transketolase_C-1umdD03
D:194-314
3b
Transketolase_C-1umdD04
D:194-314
[
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 C
Chain D
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 (247 KB)
Header - Asym.Unit
Biol.Unit 1 (242 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
1UMD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help