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.
1UDY
Asym. Unit
Info
Asym.Unit (261 KB)
Biol.Unit 1 (253 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
MEDIUM-CHAIN ACYL-COA DEHYDROGENASE WITH 3-THIAOCTANOYL-COA
Authors
:
A. Satoh, Y. Nakajima, I. Miyahara, K. Hirotsu, T. Tanaka, Y. Nishina, K. Shiga, H. Tamaoki, C. Setoyama, R. Miura
Date
:
07 May 03 (Deposition) - 09 Dec 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Mcad Complex, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Satoh, Y. Nakajima, I. Miyahara, K. Hirotsu, T. Tanaka, Y. Nishina, K. Shiga, H. Tamaoki, C. Setoyama, R. Miura
Structure Of The Transition State Analog Of Medium-Chain Acyl-Coa Dehydrogenase. Crystallographic And Molecular Orbital Studies On The Charge-Transfer Complex Of Medium-Chain Acyl-Coa Dehydrogenase With 3-Thiaoctanoyl-Coa
J. Biochem. (Tokyo) V. 134 297 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 8)
Info
All Hetero Components
1a: 3-THIAOCTANOYL-COENZYME A (CS8a)
1b: 3-THIAOCTANOYL-COENZYME A (CS8b)
1c: 3-THIAOCTANOYL-COENZYME A (CS8c)
1d: 3-THIAOCTANOYL-COENZYME A (CS8d)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
2d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CS8
4
Ligand/Ion
3-THIAOCTANOYL-COENZYME A
2
FAD
4
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:133 , VAL A:135 , THR A:136 , GLY A:141 , SER A:142 , TRP A:166 , THR A:168 , ILE A:371 , THR A:378 , GLN A:380 , CS8 A:400 , HOH A:897 , ARG B:281 , THR B:283 , PHE B:284 , HIS B:291 , ILE B:294 , GLN B:349 , VAL B:350 , GLY B:352 , GLY B:353 , GLN D:292
BINDING SITE FOR RESIDUE FAD A 399
2
AC2
SOFTWARE
GLU A:99 , LEU A:103 , TYR A:133 , GLY A:141 , SER A:142 , VAL A:144 , SER A:191 , PHE A:245 , MET A:249 , PHE A:252 , ASP A:253 , ARG A:256 , VAL A:259 , ARG A:324 , THR A:326 , TYR A:375 , GLU A:376 , GLY A:377 , ILE A:385 , ARG A:388 , FAD A:399 , HOH A:817 , HOH A:836 , HOH A:1014 , HOH A:1030
BINDING SITE FOR RESIDUE CS8 A 400
3
AC3
SOFTWARE
ARG A:281 , THR A:283 , PHE A:284 , GLN A:349 , VAL A:350 , GLY A:353 , TYR B:133 , VAL B:135 , THR B:136 , GLY B:141 , SER B:142 , TRP B:166 , THR B:168 , ILE B:371 , TYR B:375 , THR B:378 , GLN B:380 , HOH B:1029 , CS8 B:1400 , GLN C:292
BINDING SITE FOR RESIDUE FAD B 1399
4
AC4
SOFTWARE
THR B:96 , GLU B:99 , LEU B:103 , TYR B:133 , THR B:136 , GLY B:141 , SER B:142 , VAL B:144 , SER B:191 , PHE B:245 , MET B:249 , ASP B:253 , VAL B:259 , ARG B:324 , THR B:326 , TYR B:375 , GLU B:376 , GLY B:377 , ILE B:381 , ILE B:385 , ARG B:388 , FAD B:1399 , ARG C:123 , ASN C:174
BINDING SITE FOR RESIDUE CS8 B 1400
5
AC5
SOFTWARE
GLN B:292 , TYR C:133 , VAL C:135 , THR C:136 , GLY C:141 , SER C:142 , TRP C:166 , THR C:168 , ILE C:371 , THR C:378 , GLN C:380 , CS8 C:2400 , HOH C:2404 , HOH C:2424 , HOH C:2442 , ARG D:281 , THR D:283 , PHE D:284 , LEU D:288 , HIS D:291 , ILE D:294 , GLN D:349 , VAL D:350 , GLY D:352 , GLY D:353
BINDING SITE FOR RESIDUE FAD C 2399
6
AC6
SOFTWARE
GLU C:99 , LEU C:103 , TYR C:133 , GLY C:141 , SER C:142 , VAL C:144 , SER C:191 , PHE C:245 , MET C:249 , PHE C:252 , ASP C:253 , ARG C:256 , ARG C:324 , THR C:326 , TYR C:375 , GLU C:376 , GLY C:377 , ILE C:385 , ARG C:388 , FAD C:2399
BINDING SITE FOR RESIDUE CS8 C 2400
7
AC7
SOFTWARE
GLN A:292 , ARG C:281 , THR C:283 , PHE C:284 , LEU C:288 , HIS C:291 , ILE C:294 , GLN C:349 , VAL C:350 , GLY C:352 , GLY C:353 , TYR D:133 , VAL D:135 , THR D:136 , GLY D:141 , SER D:142 , TRP D:166 , THR D:168 , ILE D:371 , THR D:378 , GLN D:380 , HOH D:805 , CS8 D:3400
BINDING SITE FOR RESIDUE FAD D 3399
8
AC8
SOFTWARE
THR D:96 , GLU D:99 , ALA D:100 , LEU D:103 , TYR D:133 , GLY D:141 , SER D:142 , VAL D:144 , SER D:191 , PHE D:245 , PHE D:252 , ASP D:253 , ARG D:256 , ARG D:324 , THR D:326 , TYR D:375 , GLU D:376 , GLY D:377 , ILE D:385 , ARG D:388 , HOH D:931 , HOH D:1020 , FAD D:3399
BINDING SITE FOR RESIDUE CS8 D 3400
[
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
(2, 8)
Info
All PROSITE Patterns/Profiles
1: ACYL_COA_DH_1 (A:134-146,B:134-146,C:134-146,D:13...)
2: ACYL_COA_DH_2 (A:349-368,B:349-368,C:349-368,D:34...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ACYL_COA_DH_1
PS00072
Acyl-CoA dehydrogenases signature 1.
ACADM_PIG
159-171
4
A:134-146
B:134-146
C:134-146
D:134-146
2
ACYL_COA_DH_2
PS00073
Acyl-CoA dehydrogenases signature 2.
ACADM_PIG
374-393
4
A:349-368
B:349-368
C:349-368
D:349-368
[
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, 8)
Info
All SCOP Domains
1a: SCOP_d1udya1 (A:242-395)
1b: SCOP_d1udyb1 (B:242-393)
1c: SCOP_d1udyc1 (C:242-395)
1d: SCOP_d1udyd1 (D:242-395)
2a: SCOP_d1udya2 (A:11-241)
2b: SCOP_d1udyb2 (B:11-241)
2c: SCOP_d1udyc2 (C:11-241)
2d: SCOP_d1udyd2 (D:11-241)
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)
Pig (Sus scrofa) [TaxId: 9823]
(3)
1a
d1udya1
A:242-395
1b
d1udyb1
B:242-393
1c
d1udyc1
C:242-395
1d
d1udyd1
D:242-395
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)
Pig (Sus scrofa) [TaxId: 9823]
(3)
2a
d1udya2
A:11-241
2b
d1udyb2
B:11-241
2c
d1udyc2
C:11-241
2d
d1udyd2
D:11-241
[
close SCOP info
]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1udyA01 (A:11-130)
1b: CATH_1udyB01 (B:11-130)
1c: CATH_1udyC01 (C:11-130)
1d: CATH_1udyD01 (D:11-130)
2a: CATH_1udyA03 (A:252-395)
2b: CATH_1udyC03 (C:252-395)
2c: CATH_1udyD03 (D:252-395)
2d: CATH_1udyB03 (B:252-393)
3a: CATH_1udyA02 (A:131-251)
3b: CATH_1udyB02 (B:131-251)
3c: CATH_1udyC02 (C:131-251)
3d: CATH_1udyD02 (D:131-251)
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)
Pig (Sus scrofa)
(3)
1a
1udyA01
A:11-130
1b
1udyB01
B:11-130
1c
1udyC01
C:11-130
1d
1udyD01
D:11-130
Architecture
:
Up-down Bundle
(3216)
Topology
:
Butyryl-CoA Dehydrogenase, subunit A; domain 3
(76)
Homologous Superfamily
:
Butyryl-CoA Dehydrogenase, subunit A, domain 3
(37)
Pig (Sus scrofa)
(3)
2a
1udyA03
A:252-395
2b
1udyC03
C:252-395
2c
1udyD03
D:252-395
2d
1udyB03
B:252-393
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)
Pig (Sus scrofa)
(3)
3a
1udyA02
A:131-251
3b
1udyB02
B:131-251
3c
1udyC02
C:131-251
3d
1udyD02
D:131-251
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_Acyl_CoA_dh_1_1udyD01 (D:242-391)
1b: PFAM_Acyl_CoA_dh_1_1udyD02 (D:242-391)
1c: PFAM_Acyl_CoA_dh_1_1udyD03 (D:242-391)
1d: PFAM_Acyl_CoA_dh_1_1udyD04 (D:242-391)
2a: PFAM_Acyl_CoA_dh_M_1udyD05 (D:132-183)
2b: PFAM_Acyl_CoA_dh_M_1udyD06 (D:132-183)
2c: PFAM_Acyl_CoA_dh_M_1udyD07 (D:132-183)
2d: PFAM_Acyl_CoA_dh_M_1udyD08 (D:132-183)
3a: PFAM_Acyl_CoA_dh_N_1udyD09 (D:17-128)
3b: PFAM_Acyl_CoA_dh_N_1udyD10 (D:17-128)
3c: PFAM_Acyl_CoA_dh_N_1udyD11 (D:17-128)
3d: PFAM_Acyl_CoA_dh_N_1udyD12 (D:17-128)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Acyl-CoA_dh
(32)
Family
:
Acyl-CoA_dh_1
(24)
Sus scrofa (Pig)
(3)
1a
Acyl-CoA_dh_1-1udyD01
D:242-391
1b
Acyl-CoA_dh_1-1udyD02
D:242-391
1c
Acyl-CoA_dh_1-1udyD03
D:242-391
1d
Acyl-CoA_dh_1-1udyD04
D:242-391
Clan
:
no clan defined [family: Acyl-CoA_dh_M]
(24)
Family
:
Acyl-CoA_dh_M
(24)
Sus scrofa (Pig)
(3)
2a
Acyl-CoA_dh_M-1udyD05
D:132-183
2b
Acyl-CoA_dh_M-1udyD06
D:132-183
2c
Acyl-CoA_dh_M-1udyD07
D:132-183
2d
Acyl-CoA_dh_M-1udyD08
D:132-183
Clan
:
no clan defined [family: Acyl-CoA_dh_N]
(23)
Family
:
Acyl-CoA_dh_N
(23)
Sus scrofa (Pig)
(3)
3a
Acyl-CoA_dh_N-1udyD09
D:17-128
3b
Acyl-CoA_dh_N-1udyD10
D:17-128
3c
Acyl-CoA_dh_N-1udyD11
D:17-128
3d
Acyl-CoA_dh_N-1udyD12
D:17-128
[
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 (261 KB)
Header - Asym.Unit
Biol.Unit 1 (253 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
1UDY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help