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.
1UKW
Asym. Unit
Info
Asym.Unit (130 KB)
Biol.Unit 1 (125 KB)
Biol.Unit 2 (248 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF MEDIUM-CHAIN ACYL-COA DEHYDROGENASE FROM THERMUS THERMOPHILUS HB8
Authors
:
K. Hamada, H. Ago, S. Kuramitsu, M. Miyano, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
02 Sep 03 (Deposition) - 09 Nov 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (2x)
Keywords
:
Oxidoreductase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Hamada, H. Ago, S. Kuramitsu, M. Miyano
Crystal Structure Of Thermus Thermophilus Medium-Chain Acyl-Coa Dehydrogenase
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 3)
Info
All Hetero Components
1a: COBALT (II) ION (COa)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CO
1
Ligand/Ion
COBALT (II) ION
2
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP B:176 , HIS B:177 , HOH B:1186
BINDING SITE FOR RESIDUE CO B 411
2
AC2
SOFTWARE
PHE A:153 , LEU A:155 , SER A:156 , GLY A:161 , SER A:162 , TRP A:186 , SER A:188 , LEU A:388 , ILE A:391 , TYR A:392 , GLU A:393 , THR A:395 , GLU A:397 , LEU A:401 , HOH A:1010 , HOH A:1067 , HOH A:1201 , GLN B:309
BINDING SITE FOR RESIDUE FAD A 420
3
AC3
SOFTWARE
GLN A:309 , PHE B:153 , LEU B:155 , SER B:156 , GLY B:161 , SER B:162 , TRP B:186 , SER B:188 , LYS B:231 , LEU B:388 , ILE B:391 , TYR B:392 , GLU B:393 , GLY B:394 , THR B:395 , GLU B:397 , LEU B:401 , HOH B:1011 , HOH B:1025 , HOH B:1100 , HOH B:1149
BINDING SITE FOR RESIDUE FAD B 421
[
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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1ukwa1 (A:259-410)
1b: SCOP_d1ukwb1 (B:259-410)
2a: SCOP_d1ukwa2 (A:32-258)
2b: SCOP_d1ukwb2 (B:32-258)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Bromodomain-like
(339)
Superfamily
:
Acyl-CoA dehydrogenase C-terminal domain-like
(61)
Family
:
Medium chain acyl-CoA dehydrogenase-like, C-terminal domain
(29)
Protein domain
:
Medium chain acyl-CoA dehydrogenase, C-domain
(8)
Thermus thermophilus [TaxId: 274]
(1)
1a
d1ukwa1
A:259-410
1b
d1ukwb1
B:259-410
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Acyl-CoA dehydrogenase NM domain-like
(61)
Superfamily
:
Acyl-CoA dehydrogenase NM domain-like
(61)
Family
:
Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains
(32)
Protein domain
:
Medium chain acyl-CoA dehydrogenase, NM domains
(8)
Thermus thermophilus [TaxId: 274]
(1)
2a
d1ukwa2
A:32-258
2b
d1ukwb2
B:32-258
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1ukwA01 (A:32-147)
1b: CATH_1ukwB01 (B:32-147)
2a: CATH_1ukwA03 (A:258-410)
2b: CATH_1ukwB03 (B:258-410)
3a: CATH_1ukwA02 (A:148-257)
3b: CATH_1ukwB02 (B:148-257)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Butyryl-Coa Dehydrogenase, subunit A; domain 1
(28)
Homologous Superfamily
:
Butyryl-Coa Dehydrogenase, subunit A, domain 1
(28)
Thermus thermophilus. Organism_taxid: 274.
(2)
1a
1ukwA01
A:32-147
1b
1ukwB01
B:32-147
Architecture
:
Up-down Bundle
(3216)
Topology
:
Butyryl-CoA Dehydrogenase, subunit A; domain 3
(76)
Homologous Superfamily
:
Butyryl-CoA Dehydrogenase, subunit A, domain 3
(37)
Thermus thermophilus. Organism_taxid: 274.
(2)
2a
1ukwA03
A:258-410
2b
1ukwB03
B:258-410
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Butyryl-CoA Dehydrogenase, subunit A; domain 2
(35)
Homologous Superfamily
:
Butyryl-CoA Dehydrogenase, subunit A, domain 2
(35)
Thermus thermophilus. Organism_taxid: 274.
(2)
3a
1ukwA02
A:148-257
3b
1ukwB02
B:148-257
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Acyl_CoA_dh_1_1ukwB01 (B:259-408)
1b: PFAM_Acyl_CoA_dh_1_1ukwB02 (B:259-408)
2a: PFAM_Acyl_CoA_dh_M_1ukwB03 (B:152-203)
2b: PFAM_Acyl_CoA_dh_M_1ukwB04 (B:152-203)
3a: PFAM_Acyl_CoA_dh_N_1ukwB05 (B:37-148)
3b: PFAM_Acyl_CoA_dh_N_1ukwB06 (B:37-148)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Acyl-CoA_dh
(32)
Family
:
Acyl-CoA_dh_1
(24)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
(1)
1a
Acyl-CoA_dh_1-1ukwB01
B:259-408
1b
Acyl-CoA_dh_1-1ukwB02
B:259-408
Clan
:
no clan defined [family: Acyl-CoA_dh_M]
(24)
Family
:
Acyl-CoA_dh_M
(24)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
(1)
2a
Acyl-CoA_dh_M-1ukwB03
B:152-203
2b
Acyl-CoA_dh_M-1ukwB04
B:152-203
Clan
:
no clan defined [family: Acyl-CoA_dh_N]
(23)
Family
:
Acyl-CoA_dh_N
(23)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
(1)
3a
Acyl-CoA_dh_N-1ukwB05
B:37-148
3b
Acyl-CoA_dh_N-1ukwB06
B:37-148
[
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 (130 KB)
Header - Asym.Unit
Biol.Unit 1 (125 KB)
Header - Biol.Unit 1
Biol.Unit 2 (248 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
1UKW
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help