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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3B96
Asym. Unit
Info
Asym.Unit (102 KB)
Biol.Unit 1 (191 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(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
)
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2a: TETRADECANOYL-COA (MYAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
MYA
1
Ligand/Ion
TETRADECANOYL-COA
[
close Hetero Component info
]
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, 37)
Info
(mutated residues are not available)
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, 2)
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
1
A:175-187
2
ACYL_COA_DH_2
PS00073
Acyl-CoA dehydrogenases signature 2.
ACADV_HUMAN
435-454
1
A:395-414
[
close PROSITE info
]
Exons
(18, 18)
Info
All Exons
Exon 1.2 (A:29-52)
Exon 1.3 (A:53-74)
Exon 1.4 (A:75-99)
Exon 1.5 (A:99-120)
Exon 1.6 (A:121-165)
Exon 1.7 (A:166-214)
Exon 1.8 (A:214-257)
Exon 1.9 (A:257-299)
Exon 1.10 (A:299-365)
Exon 1.11 (A:366-400)
Exon 1.12 (A:401-429)
Exon 1.13 (A:430-445)
Exon 1.14 (A:479-484)
Exon 1.15 (A:485-517)
Exon 1.16 (A:517-541)
Exon 1.17 (A:542-566)
Exon 1.18 (A:566-590)
Exon 1.19 (A:590-615)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.2
02: Boundary 1.2/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
10: Boundary 1.10/1.11
11: Boundary 1.11/1.12
12: Boundary 1.12/1.13
13: Boundary 1.13/1.14
14: Boundary 1.14/1.15
15: Boundary 1.15/1.16
16: Boundary 1.16/1.17
17: Boundary 1.17/1.18
18: Boundary 1.18/1.19
19: Boundary 1.19/1.20b
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000356839
1a
ENSE00001486705
chr17:
7123131-7123365
235
ACADV_HUMAN
1-67
67
0
-
-
1.2
ENST00000356839
2
ENSE00001150930
chr17:
7123441-7123516
76
ACADV_HUMAN
67-92
26
1
A:29-52
24
1.3
ENST00000356839
3
ENSE00001203537
chr17:
7123783-7123848
66
ACADV_HUMAN
93-114
22
1
A:53-74
22
1.4
ENST00000356839
4
ENSE00001150924
chr17:
7123923-7123995
73
ACADV_HUMAN
115-139
25
1
A:75-99
25
1.5
ENST00000356839
5
ENSE00001150919
chr17:
7124085-7124149
65
ACADV_HUMAN
139-160
22
1
A:99-120
22
1.6
ENST00000356839
6
ENSE00001150916
chr17:
7124243-7124377
135
ACADV_HUMAN
161-205
45
1
A:121-165
45
1.7
ENST00000356839
7
ENSE00000681054
chr17:
7124857-7125001
145
ACADV_HUMAN
206-254
49
1
A:166-214
49
1.8
ENST00000356839
8
ENSE00000887266
chr17:
7125271-7125400
130
ACADV_HUMAN
254-297
44
1
A:214-257
44
1.9
ENST00000356839
9
ENSE00000887267
chr17:
7125496-7125621
126
ACADV_HUMAN
297-339
43
1
A:257-299
43
1.10
ENST00000356839
10
ENSE00000681061
chr17:
7125986-7126184
199
ACADV_HUMAN
339-405
67
1
A:299-365
67
1.11
ENST00000356839
11
ENSE00000681063
chr17:
7126452-7126556
105
ACADV_HUMAN
406-440
35
1
A:366-400
35
1.12
ENST00000356839
12
ENSE00000681066
chr17:
7126963-7127049
87
ACADV_HUMAN
441-469
29
1
A:401-429
29
1.13
ENST00000356839
13
ENSE00000681068
chr17:
7127132-7127194
63
ACADV_HUMAN
470-490
21
1
A:430-445
16
1.14
ENST00000356839
14
ENSE00000681071
chr17:
7127287-7127388
102
ACADV_HUMAN
491-524
34
1
A:479-484
6
1.15
ENST00000356839
15
ENSE00000681074
chr17:
7127465-7127562
98
ACADV_HUMAN
525-557
33
1
A:485-517
33
1.16
ENST00000356839
16
ENSE00000681076
chr17:
7127640-7127712
73
ACADV_HUMAN
557-581
25
1
A:517-541
25
1.17
ENST00000356839
17
ENSE00000681078
chr17:
7127799-7127871
73
ACADV_HUMAN
582-606
25
1
A:542-566
25
1.18
ENST00000356839
18
ENSE00000681080
chr17:
7127961-7128033
73
ACADV_HUMAN
606-630
25
1
A:566-590
25
1.19
ENST00000356839
19
ENSE00000681082
chr17:
7128128-7128203
76
ACADV_HUMAN
630-655
26
1
A:590-615
26
1.20b
ENST00000356839
20b
ENSE00001873164
chr17:
7128276-7128587
312
ACADV_HUMAN
656-701
46
0
-
-
[
close EXON info
]
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
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (102 KB)
Header - Asym.Unit
Biol.Unit 1 (191 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
3B96
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help