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2VIG
Biol. Unit 2
Info
Asym.Unit (495 KB)
Biol.Unit 1 (245 KB)
Biol.Unit 2 (246 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN SHORT-CHAIN ACYL COA DEHYDROGENASE
Authors
:
A. C. W. Pike, N. Pantic, E. Parizotto, O. Gileadi, E. Ugochukwu, F. Von Delft, J. Weigelt, C. H. Arrowsmith, A. Edwards, U. Oppermann
Date
:
30 Nov 07 (Deposition) - 25 Dec 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,L
#
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
(
#
: chains that contain no standard or modified protein/DNA/RNA residue)
Keywords
:
Fatty Acid Metabolism, Fad, Polymorphism, Flavoprotein, Mitochondrion, Disease Mutation, Lipid Metabolism, Oxidoreductase, Beta Oxidation, Transit Peptide
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. C. W. Pike, N. Pantic, E. Parizotto, O. Gileadi, E. Ugochukwu, F. Von Delft, J. Weigelt, C. H. Arrowsmith, A. Edwards, U. Oppermann
Crystal Structure Of Human Short-Chain Acyl Coa Dehydrogenase
To Be Published
[
close entry info
]
Hetero Components
(3, 14)
Info
All Hetero Components
1a: COENZYME A PERSULFIDE (COSa)
1b: COENZYME A PERSULFIDE (COSb)
1c: COENZYME A PERSULFIDE (COSc)
1d: COENZYME A PERSULFIDE (COSd)
1e: COENZYME A PERSULFIDE (COSe)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
3a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
3b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
3c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
3d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
3e: FLAVIN-ADENINE DINUCLEOTIDE (FADe)
3f: FLAVIN-ADENINE DINUCLEOTIDE (FADf)
3g: FLAVIN-ADENINE DINUCLEOTIDE (FADg)
3h: FLAVIN-ADENINE DINUCLEOTIDE (FADh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
COS
2
Ligand/Ion
COENZYME A PERSULFIDE
2
EDO
8
Ligand/Ion
1,2-ETHANEDIOL
3
FAD
4
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(14, 14)
Info
All Sites
01: AC8 (SOFTWARE)
02: AC9 (SOFTWARE)
03: BC1 (SOFTWARE)
04: BC2 (SOFTWARE)
05: BC3 (SOFTWARE)
06: BC4 (SOFTWARE)
07: BC5 (SOFTWARE)
08: BC7 (SOFTWARE)
09: BC8 (SOFTWARE)
10: CC3 (SOFTWARE)
11: CC4 (SOFTWARE)
12: CC5 (SOFTWARE)
13: CC6 (SOFTWARE)
14: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC8
SOFTWARE
PHE E:152 , LEU E:154 , SER E:155 , GLY E:160 , SER E:161 , TRP E:185 , THR E:187 , LYS E:230 , ILE E:390 , TYR E:391 , GLU E:392 , THR E:394 , GLU E:396 , LEU E:400 , HOH E:2059 , HOH E:2150 , HOH E:2158 , HOH E:2159 , HOH E:2160 , HOH E:2161 , ARG F:297 , PHE F:300 , LEU F:304 , LEU F:307 , VAL F:309 , GLN F:365 , ILE F:366 , GLY F:369 , HOH F:2112 , GLN G:308
BINDING SITE FOR RESIDUE FAD E 600
02
AC9
SOFTWARE
ARG E:297 , PHE E:300 , LEU E:304 , LEU E:307 , VAL E:309 , GLN E:365 , ILE E:366 , GLY E:369 , HOH E:2104 , PHE F:152 , LEU F:154 , SER F:155 , GLY F:160 , SER F:161 , TRP F:185 , THR F:187 , LYS F:230 , TYR F:391 , GLU F:392 , THR F:394 , GLU F:396 , COS F:605 , HOH F:2056 , HOH F:2069 , HOH F:2159 , HOH F:2160 , HOH F:2161 , GLN H:308
BINDING SITE FOR RESIDUE FAD F 600
03
BC1
SOFTWARE
SER F:155 , GLY F:160 , SER F:161 , LEU F:268 , ARG F:272 , GLU F:392 , GLY F:393 , FAD F:600 , HOH F:2055
BINDING SITE FOR RESIDUE COS F 605
04
BC2
SOFTWARE
GLN E:308 , PHE G:152 , LEU G:154 , SER G:155 , GLY G:160 , SER G:161 , TRP G:185 , ILE G:186 , THR G:187 , LYS G:230 , ILE G:387 , ILE G:390 , TYR G:391 , GLU G:392 , THR G:394 , GLU G:396 , LEU G:400 , COS G:605 , HOH G:2124 , HOH G:2125 , HOH G:2126 , HOH G:2127 , HOH G:2128 , ARG H:297 , PHE H:300 , LEU H:304 , LEU H:307 , GLN H:365 , ILE H:366 , GLY H:369 , HOH H:2089
BINDING SITE FOR RESIDUE FAD G 600
05
BC3
SOFTWARE
GLY G:160 , SER G:161 , ALA G:163 , ASN G:207 , PHE G:261 , MET G:265 , GLN G:266 , LEU G:268 , ASP G:269 , ARG G:272 , ILE G:342 , GLU G:392 , GLY G:393 , VAL G:401 , FAD G:600 , HOH G:2037 , HOH G:2078 , HOH G:2129 , HOH G:2130 , PHE H:300
BINDING SITE FOR RESIDUE COS G 605
06
BC4
SOFTWARE
GLN F:308 , ARG G:297 , PHE G:300 , LEU G:307 , GLN G:365 , ILE G:366 , GLY G:369 , HOH G:2086 , PHE H:152 , LEU H:154 , SER H:155 , GLY H:160 , SER H:161 , TRP H:185 , ILE H:186 , THR H:187 , LYS H:230 , ILE H:387 , ILE H:390 , TYR H:391 , GLU H:392 , THR H:394 , GLU H:396 , LEU H:400 , HOH H:2039 , HOH H:2046 , HOH H:2055 , HOH H:2134 , HOH H:2135
BINDING SITE FOR RESIDUE FAD H 600
07
BC5
SOFTWARE
GLN F:59 , PRO F:67 , GLN F:70 , HOH L:2001 , HOH L:2002
BINDING SITE FOR RESIDUE EDO F1414
08
BC7
SOFTWARE
LEU E:65 , PRO E:67 , GLN E:70 , HOH L:2003
BINDING SITE FOR RESIDUE EDO E1414
09
BC8
SOFTWARE
GLN H:59 , LEU H:65 , PRO H:67 , GLN H:70 , HOH L:2004
BINDING SITE FOR RESIDUE EDO H1414
10
CC3
SOFTWARE
GLU E:322 , ARG E:325 , LEU E:326 , ARG G:330 , HOH L:2007 , HOH L:2008
BINDING SITE FOR RESIDUE EDO E1415
11
CC4
SOFTWARE
ARG F:330 , GLU H:322 , ARG H:325 , LEU H:326 , HOH L:2010
BINDING SITE FOR RESIDUE EDO H1415
12
CC5
SOFTWARE
GLU E:156 , PRO E:157 , SER E:167 , GLY E:181 , THR E:182 , HOH E:2045 , HOH E:2056
BINDING SITE FOR RESIDUE EDO E1416
13
CC6
SOFTWARE
GLU D:134 , GLU F:134 , GLN F:135 , TRP F:139 , HOH L:2011
BINDING SITE FOR RESIDUE EDO F1415
14
CC7
SOFTWARE
GLU F:156 , SER F:167 , THR F:168 , GLY F:181 , THR F:182 , HOH L:2012
BINDING SITE FOR RESIDUE EDO F1416
[
close Site info
]
SAPs(SNPs)/Variants
(13, 52)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_000310 (R46W, chain E/F/G/H, )
02: VAR_013565 (G90S, chain E/F/G/H, )
03: VAR_000311 (G92C, chain E/F/G/H, )
04: VAR_000312 (R107C, chain E/F/G/H, )
05: VAR_013567 (R171W, chain E/F/G/H, )
06: VAR_000314 (W177R, chain E/F/G/H, )
07: VAR_013568 (A192V, chain E/F/G/H, )
08: VAR_000315 (S209S, chain E/F/G/H, )
09: VAR_013569 (R325W, chain E/F/G/H, )
10: VAR_013570 (S353L, chain E/F/G/H, )
11: VAR_013571 (R380W, chain E/F/G/H, )
12: VAR_000316 (R383C, chain E/F/G/H, )
13: VAR_033458 (R383H, chain E/F/G/H, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_000310
R
46
W
ACADS_HUMAN
Disease (ACADSD)
---
E/F/G/H
R
46
W
02
UniProt
VAR_013565
G
90
S
ACADS_HUMAN
Disease (ACADSD)
---
E/F/G/H
G
90
S
03
UniProt
VAR_000311
G
92
C
ACADS_HUMAN
Disease (ACADSD)
---
E/F/G/H
G
92
C
04
UniProt
VAR_000312
R
107
C
ACADS_HUMAN
Disease (ACADSD)
---
E/F/G/H
R
107
C
05
UniProt
VAR_013567
R
171
W
ACADS_HUMAN
Polymorphism
1800556
E/F/G/H
R
171
W
06
UniProt
VAR_000314
W
177
R
ACADS_HUMAN
Disease (ACADSD)
57443665
E/F/G/H
W
177
R
07
UniProt
VAR_013568
A
192
V
ACADS_HUMAN
Disease (ACADSD)
28940874
E/F/G/H
A
192
V
08
UniProt
VAR_000315
G
209
S
ACADS_HUMAN
Polymorphism
1799958
E/F/G/H
S
209
S
09
UniProt
VAR_013569
R
325
W
ACADS_HUMAN
Disease (ACADSD)
---
E/F/G/H
R
325
W
10
UniProt
VAR_013570
S
353
L
ACADS_HUMAN
Disease (ACADSD)
28941773
E/F/G/H
S
353
L
11
UniProt
VAR_013571
R
380
W
ACADS_HUMAN
Disease (ACADSD)
28940875
E/F/G/H
R
380
W
12
UniProt
VAR_000316
R
383
C
ACADS_HUMAN
Disease (ACADSD)
28940872
E/F/G/H
R
383
C
13
UniProt
VAR_033458
R
383
H
ACADS_HUMAN
Polymorphism
35233375
E/F/G/H
R
383
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: ACYL_COA_DH_1 (E:153-165,F:153-165,G:153-165,H:15...)
2: ACYL_COA_DH_2 (E:365-384,F:365-384,G:365-384,H:36...)
;
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.
ACADS_HUMAN
153-165
4
-
-
-
-
E:153-165
F:153-165
G:153-165
H:153-165
2
ACYL_COA_DH_2
PS00073
Acyl-CoA dehydrogenases signature 2.
ACADS_HUMAN
365-384
4
-
-
-
-
E:365-384
F:365-384
G:365-384
H:365-384
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 16)
Info
All SCOP Domains
1a: SCOP_d2viga2 (A:259-412)
1b: SCOP_d2vigb2 (B:259-411)
1c: SCOP_d2vigc2 (C:259-418)
1d: SCOP_d2vigd2 (D:259-413)
1e: SCOP_d2vige2 (E:259-413)
1f: SCOP_d2vigf2 (F:259-413)
1g: SCOP_d2vigg2 (G:259-411)
1h: SCOP_d2vigh2 (H:259-413)
2a: SCOP_d2viga1 (A:34-258)
2b: SCOP_d2vigb1 (B:34-258)
2c: SCOP_d2vigc1 (C:34-258)
2d: SCOP_d2vigd1 (D:34-258)
2e: SCOP_d2vige1 (E:34-258)
2f: SCOP_d2vigf1 (F:34-258)
2g: SCOP_d2vigg1 (G:34-258)
2h: SCOP_d2vigh1 (H:34-258)
View:
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Classes
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)
(
)
Folds
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)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Bromodomain-like
(339)
Superfamily
:
Acyl-CoA dehydrogenase C-terminal domain-like
(61)
Family
:
automated matches
(29)
Protein domain
:
automated matches
(29)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d2viga2
A:259-412
1b
d2vigb2
B:259-411
1c
d2vigc2
C:259-418
1d
d2vigd2
D:259-413
1e
d2vige2
E:259-413
1f
d2vigf2
F:259-413
1g
d2vigg2
G:259-411
1h
d2vigh2
H:259-413
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
:
automated matches
(10)
Human (Homo sapiens) [TaxId: 9606]
(3)
2a
d2viga1
A:34-258
2b
d2vigb1
B:34-258
2c
d2vigc1
C:34-258
2d
d2vigd1
D:34-258
2e
d2vige1
E:34-258
2f
d2vigf1
F:34-258
2g
d2vigg1
G:34-258
2h
d2vigh1
H:34-258
[
close SCOP info
]
CATH Domains
(3, 24)
Info
all CATH domains
1a: CATH_2vigA01 (A:34-149)
1b: CATH_2vigC01 (C:34-149)
1c: CATH_2vigD01 (D:34-149)
1d: CATH_2vigE01 (E:34-149)
1e: CATH_2vigF01 (F:34-149)
1f: CATH_2vigG01 (G:34-149)
1g: CATH_2vigH01 (H:34-149)
1h: CATH_2vigB01 (B:34-149)
2a: CATH_2vigA03 (A:268-408)
2b: CATH_2vigB03 (B:268-408)
2c: CATH_2vigC03 (C:268-408)
2d: CATH_2vigD03 (D:268-408)
2e: CATH_2vigE03 (E:268-408)
2f: CATH_2vigF03 (F:268-408)
2g: CATH_2vigG03 (G:268-408)
2h: CATH_2vigH03 (H:268-408)
3a: CATH_2vigG02 (G:150-267)
3b: CATH_2vigD02 (D:150-267)
3c: CATH_2vigA02 (A:150-267)
3d: CATH_2vigE02 (E:150-267)
3e: CATH_2vigC02 (C:150-267)
3f: CATH_2vigF02 (F:150-267)
3g: CATH_2vigH02 (H:150-267)
3h: CATH_2vigB02 (B:150-267)
View:
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Architectures
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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)
Human (Homo sapiens)
(10)
1a
2vigA01
A:34-149
1b
2vigC01
C:34-149
1c
2vigD01
D:34-149
1d
2vigE01
E:34-149
1e
2vigF01
F:34-149
1f
2vigG01
G:34-149
1g
2vigH01
H:34-149
1h
2vigB01
B:34-149
Architecture
:
Up-down Bundle
(3216)
Topology
:
Butyryl-CoA Dehydrogenase, subunit A; domain 3
(76)
Homologous Superfamily
:
Butyryl-CoA Dehydrogenase, subunit A, domain 3
(37)
Human (Homo sapiens)
(13)
2a
2vigA03
A:268-408
2b
2vigB03
B:268-408
2c
2vigC03
C:268-408
2d
2vigD03
D:268-408
2e
2vigE03
E:268-408
2f
2vigF03
F:268-408
2g
2vigG03
G:268-408
2h
2vigH03
H:268-408
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)
Human (Homo sapiens)
(14)
3a
2vigG02
G:150-267
3b
2vigD02
D:150-267
3c
2vigA02
A:150-267
3d
2vigE02
E:150-267
3e
2vigC02
C:150-267
3f
2vigF02
F:150-267
3g
2vigH02
H:150-267
3h
2vigB02
B:150-267
[
close CATH info
]
Pfam Domains
(3, 24)
Info
all PFAM domains
1a: PFAM_Acyl_CoA_dh_1_2vigH01 (H:258-407)
1b: PFAM_Acyl_CoA_dh_1_2vigH02 (H:258-407)
1c: PFAM_Acyl_CoA_dh_1_2vigH03 (H:258-407)
1d: PFAM_Acyl_CoA_dh_1_2vigH04 (H:258-407)
1e: PFAM_Acyl_CoA_dh_1_2vigH05 (H:258-407)
1f: PFAM_Acyl_CoA_dh_1_2vigH06 (H:258-407)
1g: PFAM_Acyl_CoA_dh_1_2vigH07 (H:258-407)
1h: PFAM_Acyl_CoA_dh_1_2vigH08 (H:258-407)
2a: PFAM_Acyl_CoA_dh_M_2vigH09 (H:151-201)
2b: PFAM_Acyl_CoA_dh_M_2vigH10 (H:151-201)
2c: PFAM_Acyl_CoA_dh_M_2vigH11 (H:151-201)
2d: PFAM_Acyl_CoA_dh_M_2vigH12 (H:151-201)
2e: PFAM_Acyl_CoA_dh_M_2vigH13 (H:151-201)
2f: PFAM_Acyl_CoA_dh_M_2vigH14 (H:151-201)
2g: PFAM_Acyl_CoA_dh_M_2vigH15 (H:151-201)
2h: PFAM_Acyl_CoA_dh_M_2vigH16 (H:151-201)
3a: PFAM_Acyl_CoA_dh_N_2vigH17 (H:35-147)
3b: PFAM_Acyl_CoA_dh_N_2vigH18 (H:35-147)
3c: PFAM_Acyl_CoA_dh_N_2vigH19 (H:35-147)
3d: PFAM_Acyl_CoA_dh_N_2vigH20 (H:35-147)
3e: PFAM_Acyl_CoA_dh_N_2vigH21 (H:35-147)
3f: PFAM_Acyl_CoA_dh_N_2vigH22 (H:35-147)
3g: PFAM_Acyl_CoA_dh_N_2vigH23 (H:35-147)
3h: PFAM_Acyl_CoA_dh_N_2vigH24 (H:35-147)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Acyl-CoA_dh
(32)
Family
:
Acyl-CoA_dh_1
(24)
Homo sapiens (Human)
(10)
1a
Acyl-CoA_dh_1-2vigH01
H:258-407
1b
Acyl-CoA_dh_1-2vigH02
H:258-407
1c
Acyl-CoA_dh_1-2vigH03
H:258-407
1d
Acyl-CoA_dh_1-2vigH04
H:258-407
1e
Acyl-CoA_dh_1-2vigH05
H:258-407
1f
Acyl-CoA_dh_1-2vigH06
H:258-407
1g
Acyl-CoA_dh_1-2vigH07
H:258-407
1h
Acyl-CoA_dh_1-2vigH08
H:258-407
Clan
:
no clan defined [family: Acyl-CoA_dh_M]
(24)
Family
:
Acyl-CoA_dh_M
(24)
Homo sapiens (Human)
(10)
2a
Acyl-CoA_dh_M-2vigH09
H:151-201
2b
Acyl-CoA_dh_M-2vigH10
H:151-201
2c
Acyl-CoA_dh_M-2vigH11
H:151-201
2d
Acyl-CoA_dh_M-2vigH12
H:151-201
2e
Acyl-CoA_dh_M-2vigH13
H:151-201
2f
Acyl-CoA_dh_M-2vigH14
H:151-201
2g
Acyl-CoA_dh_M-2vigH15
H:151-201
2h
Acyl-CoA_dh_M-2vigH16
H:151-201
Clan
:
no clan defined [family: Acyl-CoA_dh_N]
(23)
Family
:
Acyl-CoA_dh_N
(23)
Homo sapiens (Human)
(10)
3a
Acyl-CoA_dh_N-2vigH17
H:35-147
3b
Acyl-CoA_dh_N-2vigH18
H:35-147
3c
Acyl-CoA_dh_N-2vigH19
H:35-147
3d
Acyl-CoA_dh_N-2vigH20
H:35-147
3e
Acyl-CoA_dh_N-2vigH21
H:35-147
3f
Acyl-CoA_dh_N-2vigH22
H:35-147
3g
Acyl-CoA_dh_N-2vigH23
H:35-147
3h
Acyl-CoA_dh_N-2vigH24
H:35-147
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