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1WDK
Asym. Unit
Info
Asym.Unit (365 KB)
Biol.Unit 1 (358 KB)
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(1)
Title
:
FATTY ACID BETA-OXIDATION MULTIENZYME COMPLEX FROM PSEUDOMONAS FRAGI, FORM I (NATIVE2)
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
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Alpha2Beta2 Heterotetrameric Complex, Lyase, Oxidoreductase/Transferase Complex, Lyase, Oxidoreductase/Transferase Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
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
)
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Hetero Components
(5, 11)
Info
All Hetero Components
1a: ACETYL COENZYME *A (ACOa)
1b: ACETYL COENZYME *A (ACOb)
2a: MERCURY (II) ION (HGa)
2b: MERCURY (II) ION (HGb)
3a: 3,6,9,12,15-PENTAOXATRICOSAN-1-OL (N8Ea)
3b: 3,6,9,12,15-PENTAOXATRICOSAN-1-OL (N8Eb)
3c: 3,6,9,12,15-PENTAOXATRICOSAN-1-OL (N8Ec)
3d: 3,6,9,12,15-PENTAOXATRICOSAN-1-OL (N8Ed)
4a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
4b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
5a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACO
2
Ligand/Ion
ACETYL COENZYME *A
2
HG
2
Ligand/Ion
MERCURY (II) ION
3
N8E
4
Ligand/Ion
3,6,9,12,15-PENTAOXATRICOSAN-1-OL
4
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
5
ZN
1
Ligand/Ion
ZINC ION
[
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]
Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS D:95 , MET D:151 , PHE D:349 , ACO D:4001
BINDING SITE FOR RESIDUE HG D 1
02
AC2
SOFTWARE
CYS C:95 , MET C:151 , PHE C:349 , ACO C:3001
BINDING SITE FOR RESIDUE HG C 392
03
AC3
SOFTWARE
HIS A:550 , ASP A:573 , GLU D:266 , VAL D:391
BINDING SITE FOR RESIDUE ZN A 716
04
AC4
SOFTWARE
CYS C:95 , MET C:130 , MET C:151 , HIS C:177 , ARG C:215 , THR C:218 , LEU C:223 , PHE C:230 , ALA C:239 , GLY C:240 , SER C:243 , ILE C:245 , MET C:284 , ALA C:314 , PHE C:315 , HIS C:347 , CYS C:377 , HG C:392 , HOH C:3206
BINDING SITE FOR RESIDUE ACO C 3001
05
AC5
SOFTWARE
HG D:1 , CYS D:95 , MET D:130 , MET D:151 , HIS D:177 , ARG D:215 , THR D:218 , LEU D:223 , ALA D:239 , GLY D:240 , SER D:243 , MET D:284 , ASN D:312 , ALA D:314 , PHE D:315 , HIS D:347 , CYS D:377 , GLY D:379 , HOH D:4152 , HOH D:4155 , HOH D:4169 , HOH D:4174
BINDING SITE FOR RESIDUE ACO D 4001
06
AC6
SOFTWARE
GLY A:321 , ALA A:322 , ILE A:324 , MET A:325 , ASP A:344 , ILE A:345 , ASN A:346 , GLY A:349 , VAL A:401 , GLU A:403 , LYS A:408 , VAL A:411 , ASN A:428 , THR A:429 , SER A:430 , PHE A:452 , ASN A:454 , HOH A:1087 , HOH A:1177
BINDING SITE FOR RESIDUE NAD A 1001
07
AC7
SOFTWARE
MET A:459 , ASN A:501 , VAL A:659 , TYR A:660 , GLY A:661 , ILE A:662
BINDING SITE FOR RESIDUE N8E A 1002
08
AC8
SOFTWARE
GLY A:68 , ALA A:69 , ASP A:70 , ILE A:71 , PHE A:74 , GLY A:116 , GLY A:117 , PRO A:139 , GLU A:140 , LEU A:143 , GLN A:298 , LYS A:305
BINDING SITE FOR RESIDUE N8E A 1003
09
AC9
SOFTWARE
GLY B:321 , ALA B:322 , ILE B:324 , MET B:325 , ASP B:344 , ILE B:345 , VAL B:401 , GLU B:403 , LYS B:408 , VAL B:411 , ASN B:428 , THR B:429 , SER B:430 , ASN B:454 , HOH B:2046 , HOH B:2288 , HOH B:2312
BINDING SITE FOR RESIDUE NAD B 2001
10
BC1
SOFTWARE
MET B:459 , PRO B:460 , ASN B:501 , MET B:535 , VAL B:659 , TYR B:660 , GLY B:661 , GLY B:663
BINDING SITE FOR RESIDUE N8E B 2002
11
BC2
SOFTWARE
ARG B:34 , LEU B:37 , GLU B:73 , ASN B:77 , LEU B:80 , GLY B:88 , GLU B:120 , GLU B:140 , GLY B:148 , PHE B:149 , HOH B:2309
BINDING SITE FOR RESIDUE N8E B 2003
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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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
[
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Exons
(0, 0)
Info
All Exons
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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_d1wdka1 (A:497-620)
1b: SCOP_d1wdka2 (A:621-715)
1c: SCOP_d1wdkb1 (B:497-620)
1d: SCOP_d1wdkb2 (B:621-715)
2a: SCOP_d1wdka4 (A:1-310)
2b: SCOP_d1wdkb4 (B:1-310)
3a: SCOP_d1wdka3 (A:311-496)
3b: SCOP_d1wdkb3 (B:311-496)
4a: SCOP_d1wdkc1 (C:2-263)
4b: SCOP_d1wdkc2 (C:264-391)
4c: SCOP_d1wdkd1 (D:2-263)
4d: SCOP_d1wdkd2 (D:264-391)
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)
(
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)
(
)
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
d1wdka1
A:497-620
1b
d1wdka2
A:621-715
1c
d1wdkb1
B:497-620
1d
d1wdkb2
B: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
d1wdka4
A:1-310
2b
d1wdkb4
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
d1wdka3
A:311-496
3b
d1wdkb3
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
d1wdkc1
C:2-263
4b
d1wdkc2
C:264-391
4c
d1wdkd1
D:2-263
4d
d1wdkd2
D:264-391
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1wdkC02 (C:138-187,C:272-388)
1b: CATH_1wdkD02 (D:138-187,D:272-388)
1c: CATH_1wdkC01 (C:2-130,C:188-271)
1d: CATH_1wdkD01 (D:2-130,D:188-271)
2a: CATH_1wdkA02 (A:314-497)
2b: CATH_1wdkB02 (B:314-497)
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Homologous Superfamilies
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)
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)
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
1wdkC02
C:138-187,C:272-388
1b
1wdkD02
D:138-187,D:272-388
1c
1wdkC01
C:2-130,C:188-271
1d
1wdkD01
D:2-130,D:188-271
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Pseudomonas fragi. Organism_taxid: 296.
(10)
2a
1wdkA02
A:314-497
2b
1wdkB02
B:314-497
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asym.Unit (365 KB)
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