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.
1WDL
Asym. Unit
Info
Asym.Unit (314 KB)
Biol.Unit 1 (306 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
FATTY ACID BETA-OXIDATION MULTIENZYME COMPLEX FROM PSEUDOMONAS FRAGI, FORM II (NATIVE4)
Authors
:
M. Ishikawa, D. Tsuchiya, T. Oyama, Y. Tsunaka, K. Morikawa
Date
:
17 May 04 (Deposition) - 27 Jul 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Alpha2Beta2 Heterotetrameric Complex, Lyase, Oxidoreductase/Transferase Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Ishikawa, D. Tsuchiya, T. Oyama, Y. Tsunaka, K. Morikawa
Structural Basis For Channelling Mechanism Of A Fatty Acid Beta-Oxidation Multienzyme Complex
Embo J. V. 23 2745 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 7)
Info
All Hetero Components
1a: ACETYL COENZYME *A (ACOa)
1b: ACETYL COENZYME *A (ACOb)
2a: 3,6,9,12,15-PENTAOXATRICOSAN-1-OL (N8Ea)
2b: 3,6,9,12,15-PENTAOXATRICOSAN-1-OL (N8Eb)
2c: 3,6,9,12,15-PENTAOXATRICOSAN-1-OL (N8Ec)
3a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
3b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACO
2
Ligand/Ion
ACETYL COENZYME *A
2
N8E
3
Ligand/Ion
3,6,9,12,15-PENTAOXATRICOSAN-1-OL
3
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU C:223 , PHE C:230 , ALA C:239 , GLY C:240 , ILE C:245
BINDING SITE FOR RESIDUE ACO C 3001
2
AC2
SOFTWARE
CYS D:95 , MET D:151 , HIS D:177 , ARG D:215 , THR D:218 , SER D:243 , ALA D:314 , PHE D:315 , HIS D:347 , PHE D:349 , CYS D:377
BINDING SITE FOR RESIDUE ACO D 4001
3
AC3
SOFTWARE
ALA A:322 , ILE A:324 , MET A:325 , ASP A:344 , ILE A:345 , ALA A:400 , VAL A:401 , GLU A:403 , LYS A:408 , VAL A:411 , ASN A:428 , THR A:429 , SER A:430
BINDING SITE FOR RESIDUE NAD A 1001
4
AC4
SOFTWARE
ASN A:454 , MET A:459 , ASN A:501 , MET A:535 , VAL A:659 , TYR A:660
BINDING SITE FOR RESIDUE N8E A 1002
5
AC5
SOFTWARE
ASN A:38 , ALA A:69 , PHE A:74 , ASN A:77 , GLY A:88 , ASN A:89 , GLU A:91 , GLY A:116 , GLY A:117 , GLU A:140
BINDING SITE FOR RESIDUE N8E A 1003
6
AC6
SOFTWARE
ILE A:345 , LEU A:386 , ASN A:404 , ASN B:393 , HIS C:181 , THR C:184 , ASP C:209
BINDING SITE FOR RESIDUE N8E A 1004
7
AC7
SOFTWARE
ALA B:322 , ILE B:324 , MET B:325 , ASP B:344 , ILE B:345 , ASN B:346 , ALA B:400 , VAL B:401 , GLU B:403 , LYS B:408 , VAL B:411 , ASN B:428 , THR B:429 , SER B:430 , ASN B:454
BINDING SITE FOR RESIDUE NAD B 2001
[
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
(5, 10)
Info
All PROSITE Patterns/Profiles
1: THIOLASE_1 (C:91-109,D:91-109)
2: ENOYL_COA_HYDRATASE (A:107-127,B:107-127)
3: THIOLASE_2 (C:337-353,D:337-353)
4: THIOLASE_3 (C:372-385,D:372-385)
5: 3HCDH (A:494-518,B:494-518)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THIOLASE_1
PS00098
Thiolases acyl-enzyme intermediate signature.
FADA_PSEFR
91-109
2
C:91-109
D:91-109
2
ENOYL_COA_HYDRATASE
PS00166
Enoyl-CoA hydratase/isomerase signature.
FADB_PSEFR
107-127
2
A:107-127
B:107-127
3
THIOLASE_2
PS00737
Thiolases signature 2.
FADA_PSEFR
337-353
2
C:337-353
D:337-353
4
THIOLASE_3
PS00099
Thiolases active site.
FADA_PSEFR
372-385
2
C:372-385
D:372-385
5
3HCDH
PS00067
3-hydroxyacyl-CoA dehydrogenase signature.
FADB_PSEFR
494-518
2
A:494-518
B:494-518
[
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
(4, 12)
Info
All SCOP Domains
1a: SCOP_d1wdla1 (A:497-620)
1b: SCOP_d1wdlb1 (B:497-620)
1c: SCOP_d1wdlb2 (B:621-715)
1d: SCOP_d1wdla2 (A:621-715)
2a: SCOP_d1wdla4 (A:1-310)
2b: SCOP_d1wdlb4 (B:1-310)
3a: SCOP_d1wdla3 (A:311-496)
3b: SCOP_d1wdlb3 (B:311-496)
4a: SCOP_d1wdlc1 (C:2-263)
4b: SCOP_d1wdld1 (D:2-263)
4c: SCOP_d1wdld2 (D:264-391)
4d: SCOP_d1wdlc2 (C:264-391)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Superfamily
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Family
:
HCDH C-domain-like
(16)
Protein domain
:
Fatty oxidation complex alpha subunit, C-terminal domain
(4)
Pseudomonas fragi [TaxId: 296]
(4)
1a
d1wdla1
A:497-620
1b
d1wdlb1
B:497-620
1c
d1wdlb2
B:621-715
1d
d1wdla2
A:621-715
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
ClpP/crotonase
(207)
Superfamily
:
ClpP/crotonase
(207)
Family
:
Crotonase-like
(39)
Protein domain
:
Fatty oxidation complex alpha subunit, N-terminal domain
(4)
Pseudomonas fragi [TaxId: 296]
(4)
2a
d1wdla4
A:1-310
2b
d1wdlb4
B:1-310
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
6-phosphogluconate dehydrogenase-like, N-terminal domain
(69)
Protein domain
:
Fatty oxidation complex alpha subunit, middle domain
(4)
Pseudomonas fragi [TaxId: 296]
(4)
3a
d1wdla3
A:311-496
3b
d1wdlb3
B:311-496
Fold
:
Thiolase-like
(231)
Superfamily
:
Thiolase-like
(231)
Family
:
Thiolase-related
(67)
Protein domain
:
Fatty oxidation complex beta subunit (3-ketoacyl-CoA thiolase)
(4)
Pseudomonas fragi [TaxId: 296]
(4)
4a
d1wdlc1
C:2-263
4b
d1wdld1
D:2-263
4c
d1wdld2
D:264-391
4d
d1wdlc2
C:264-391
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1wdlC02 (C:138-187,C:272-388)
1b: CATH_1wdlC01 (C:2-130,C:188-271)
1c: CATH_1wdlD01 (D:2-130,D:188-271)
1d: CATH_1wdlD02 (D:138-187,D:272-388)
2a: CATH_1wdlA02 (A:314-497)
2b: CATH_1wdlB02 (B:317-497)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Peroxisomal Thiolase; Chain A, domain 1
(130)
Homologous Superfamily
:
[code=3.40.47.10, no name defined]
(130)
Pseudomonas fragi. Organism_taxid: 296.
(4)
1a
1wdlC02
C:138-187,C:272-388
1b
1wdlC01
C:2-130,C:188-271
1c
1wdlD01
D:2-130,D:188-271
1d
1wdlD02
D:138-187,D:272-388
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Pseudomonas fragi. Organism_taxid: 296.
(10)
2a
1wdlA02
A:314-497
2b
1wdlB02
B:317-497
[
close CATH info
]
Pfam Domains
(5, 10)
Info
all PFAM domains
1a: PFAM_3HCDH_1wdlB01 (B:497-592)
1b: PFAM_3HCDH_1wdlB02 (B:497-592)
2a: PFAM_ECH_1wdlB03 (B:10-268)
2b: PFAM_ECH_1wdlB04 (B:10-268)
3a: PFAM_3HCDH_N_1wdlB05 (B:316-495)
3b: PFAM_3HCDH_N_1wdlB06 (B:316-495)
4a: PFAM_Thiolase_C_1wdlD01 (D:265-390)
4b: PFAM_Thiolase_C_1wdlD02 (D:265-390)
5a: PFAM_Thiolase_N_1wdlD03 (D:5-258)
5b: PFAM_Thiolase_N_1wdlD04 (D:5-258)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
6PGD_C
(47)
Family
:
3HCDH
(12)
Pseudomonas fragi
(2)
1a
3HCDH-1wdlB01
B:497-592
1b
3HCDH-1wdlB02
B:497-592
Clan
:
ClpP_crotonase
(88)
Family
:
ECH
(52)
Pseudomonas fragi
(2)
2a
ECH-1wdlB03
B:10-268
2b
ECH-1wdlB04
B:10-268
Clan
:
NADP_Rossmann
(1239)
Family
:
3HCDH_N
(12)
Pseudomonas fragi
(2)
3a
3HCDH_N-1wdlB05
B:316-495
3b
3HCDH_N-1wdlB06
B:316-495
Clan
:
Thiolase
(72)
Family
:
Thiolase_C
(23)
Pseudomonas fragi
(2)
4a
Thiolase_C-1wdlD01
D:265-390
4b
Thiolase_C-1wdlD02
D:265-390
Family
:
Thiolase_N
(23)
Pseudomonas fragi
(2)
5a
Thiolase_N-1wdlD03
D:5-258
5b
Thiolase_N-1wdlD04
D:5-258
[
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 (314 KB)
Header - Asym.Unit
Biol.Unit 1 (306 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
1WDL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help