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3B96
Biol. Unit 1
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Asym.Unit (102 KB)
Biol.Unit 1 (191 KB)
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(1)
Title
:
STRUCTURAL BASIS FOR SUBSTRATE FATTY-ACYL CHAIN SPECIFICITY: CRYSTAL STRUCTURE OF HUMAN VERY-LONG-CHAIN ACYL-COA DEHYDROGENASE
Authors
:
R. P. Mcandrew, Y. Wang, A. W. Mohsen, M. He, J. Vockley, J. J. Kim
Date
:
02 Nov 07 (Deposition) - 12 Feb 08 (Release) - 09 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.91
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Acyl-Coa, Fatty Acid Beta-Oxidation, Dehydrogenase, Very Long Chain, Mitochondria, Membrane, Acetylation, Alternative Splicing, Cardiomyopathy, Disease Mutation, Fad, Fatty Acid Metabolism, Flavoprotein, Lipid Metabolism, Mitochondrion, Oxidoreductase, Polymorphism, Transit Peptide, Ubl Conjugation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. P. Mcandrew, Y. Wang, A. W. Mohsen, M. He, J. Vockley, J. J. Kim
Structural Basis For Substrate Fatty Acyl Chain Specificity: Crystal Structure Of Human Very-Long-Chain Acyl-Coa Dehydrogenase.
J. Biol. Chem. V. 283 9435 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2a: TETRADECANOYL-COA (MYAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
MYA
2
Ligand/Ion
TETRADECANOYL-COA
[
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]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:120 , VAL A:124 , GLY A:135 , ILE A:144 , LEU A:297 , PHE A:421 , GLU A:422 , GLY A:423 , FAD A:616 , HOH A:1002
BINDING SITE FOR RESIDUE MYA A 1
2
AC2
SOFTWARE
MYA A:1 , PHE A:174 , LEU A:176 , THR A:177 , GLY A:182 , SER A:183 , TRP A:209 , ILE A:210 , SER A:211 , ARG A:326 , GLN A:328 , PHE A:329 , ILE A:333 , PHE A:336 , GLN A:395 , ILE A:396 , GLY A:399 , ILE A:417 , PHE A:421 , THR A:424 , ASP A:426 , ILE A:427 , GLN A:522 , HOH A:639 , HOH A:654 , HOH A:668 , HOH A:680
BINDING SITE FOR RESIDUE FAD A 616
[
close Site info
]
SAPs(SNPs)/Variants
(37, 74)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_000332 (T118N, chain A, )
02: VAR_000333 (Q119R, chain A, )
03: VAR_000334 (V134M, chain A, )
04: VAR_000335 (G145S, chain A, )
05: VAR_010101 (A173P, chain A, )
06: VAR_000336 (E178K, chain A, )
07: VAR_000337 (L203R, chain A, )
08: VAR_010102 (K207E, chain A, )
09: VAR_000338 (K207T, chain A, )
10: VAR_000339 (T220M, chain A, )
11: VAR_000341 (A241D, chain A, )
12: VAR_000342 (V243A, chain A, )
13: VAR_000343 (G250D, chain A, )
14: VAR_000344 (G254E, chain A, )
15: VAR_000345 (K259N, chain A, )
16: VAR_000347 (V277A, chain A, )
17: VAR_000348 (M312V, chain A, )
18: VAR_011990 (A319S, chain A, )
19: VAR_000349 (R326C, chain A, )
20: VAR_000350 (R326H, chain A, )
21: VAR_000352 (K342Q, chain A, )
22: VAR_000353 (D365H, chain A, )
23: VAR_000354 (G401D, chain A, )
24: VAR_000355 (R410H, chain A, )
25: VAR_000356 (R413Q, chain A, )
26: VAR_000357 (D414N, chain A, )
27: VAR_000358 (R416H, chain A, )
28: VAR_010103 (F418L, chain A, )
29: VAR_000359 (R419W, chain A, )
30: VAR_000360 (G423E, chain A, )
31: VAR_000361 (R429Q, chain A, )
32: VAR_000362 (R429W, chain A, )
33: VAR_010105 (E494K, chain A, )
34: VAR_000364 (L562I, chain A, )
35: VAR_000365 (R573W, chain A, )
36: VAR_010106 (R575Q, chain A, )
37: VAR_011991 (S583F, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_000332
T
158
N
ACADV_HUMAN
Disease (ACADVLD)
---
A
T
118
N
02
UniProt
VAR_000333
Q
159
R
ACADV_HUMAN
Disease (ACADVLD)
---
A
Q
119
R
03
UniProt
VAR_000334
V
174
M
ACADV_HUMAN
Disease (ACADVLD)
---
A
V
134
M
04
UniProt
VAR_000335
G
185
S
ACADV_HUMAN
Disease (ACADVLD)
---
A
G
145
S
05
UniProt
VAR_010101
A
213
P
ACADV_HUMAN
Disease (ACADVLD)
140629318
A
A
173
P
06
UniProt
VAR_000336
E
218
K
ACADV_HUMAN
Disease (ACADVLD)
---
A
E
178
K
07
UniProt
VAR_000337
L
243
R
ACADV_HUMAN
Disease (ACADVLD)
---
A
L
203
R
08
UniProt
VAR_010102
K
247
E
ACADV_HUMAN
Disease (ACADVLD)
---
A
K
207
E
09
UniProt
VAR_000338
K
247
T
ACADV_HUMAN
Disease (ACADVLD)
---
A
K
207
T
10
UniProt
VAR_000339
T
260
M
ACADV_HUMAN
Disease (ACADVLD)
113994168
A
T
220
M
11
UniProt
VAR_000341
A
281
D
ACADV_HUMAN
Disease (ACADVLD)
---
A
A
241
D
12
UniProt
VAR_000342
V
283
A
ACADV_HUMAN
Disease (ACADVLD)
113994167
A
V
243
A
13
UniProt
VAR_000343
G
290
D
ACADV_HUMAN
Disease (ACADVLD)
---
A
G
250
D
14
UniProt
VAR_000344
G
294
E
ACADV_HUMAN
Disease (ACADVLD)
200573371
A
G
254
E
15
UniProt
VAR_000345
K
299
N
ACADV_HUMAN
Disease (ACADVLD)
---
A
K
259
N
16
UniProt
VAR_000347
V
317
A
ACADV_HUMAN
Disease (ACADVLD)
---
A
V
277
A
17
UniProt
VAR_000348
M
352
V
ACADV_HUMAN
Disease (ACADVLD)
---
A
M
312
V
18
UniProt
VAR_011990
A
359
S
ACADV_HUMAN
Polymorphism
1051701
A
A
319
S
19
UniProt
VAR_000349
R
366
C
ACADV_HUMAN
Disease (ACADVLD)
---
A
R
326
C
20
UniProt
VAR_000350
R
366
H
ACADV_HUMAN
Disease (ACADVLD)
112406105
A
R
326
H
21
UniProt
VAR_000352
K
382
Q
ACADV_HUMAN
Disease (ACADVLD)
118204015
A
K
342
Q
22
UniProt
VAR_000353
D
405
H
ACADV_HUMAN
Disease (ACADVLD)
---
A
D
365
H
23
UniProt
VAR_000354
G
441
D
ACADV_HUMAN
Disease (ACADVLD)
2309689
A
G
401
D
24
UniProt
VAR_000355
R
450
H
ACADV_HUMAN
Disease (ACADVLD)
118204016
A
R
410
H
25
UniProt
VAR_000356
R
453
Q
ACADV_HUMAN
Disease (ACADVLD)
138058572
A
R
413
Q
26
UniProt
VAR_000357
D
454
N
ACADV_HUMAN
Disease (ACADVLD)
---
A
D
414
N
27
UniProt
VAR_000358
R
456
H
ACADV_HUMAN
Disease (ACADVLD)
---
A
R
416
H
28
UniProt
VAR_010103
F
458
L
ACADV_HUMAN
Disease (ACADVLD)
118204017
A
F
418
L
29
UniProt
VAR_000359
R
459
W
ACADV_HUMAN
Disease (ACADVLD)
---
A
R
419
W
30
UniProt
VAR_000360
G
463
E
ACADV_HUMAN
Disease (ACADVLD)
200366828
A
G
423
E
31
UniProt
VAR_000361
R
469
Q
ACADV_HUMAN
Disease (ACADVLD)
---
A
R
429
Q
32
UniProt
VAR_000362
R
469
W
ACADV_HUMAN
Disease (ACADVLD)
113994170
A
R
429
W
33
UniProt
VAR_010105
E
534
K
ACADV_HUMAN
Disease (ACADVLD)
2230180
A
E
494
K
34
UniProt
VAR_000364
L
602
I
ACADV_HUMAN
Disease (ACADVLD)
---
A
L
562
I
35
UniProt
VAR_000365
R
613
W
ACADV_HUMAN
Disease (ACADVLD)
118204014
A
R
573
W
36
UniProt
VAR_010106
R
615
Q
ACADV_HUMAN
Disease (ACADVLD)
148584617
A
R
575
Q
37
UniProt
VAR_011991
S
623
F
ACADV_HUMAN
Polymorphism
13383
A
S
583
F
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: ACYL_COA_DH_1 (A:175-187)
2: ACYL_COA_DH_2 (A:395-414)
;
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.
ACADV_HUMAN
215-227
2
A:175-187
2
ACYL_COA_DH_2
PS00073
Acyl-CoA dehydrogenases signature 2.
ACADV_HUMAN
435-454
2
A:395-414
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_3b96A01 (A:29-50,A:287-445)
2a: CATH_3b96A03 (A:172-286)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
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)
1a
3b96A01
A:29-50,A:287-445
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)
2a
3b96A03
A:172-286
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Atom Selection
(currently selected atoms:
all
)
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Nucleic
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Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
Asymmetric Unit 2
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