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.
1IVH
Asym. Unit
Info
Asym.Unit (258 KB)
Biol.Unit 1 (250 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF HUMAN ISOVALERYL-COA DEHYDROGENASE AT 2.6 ANGSTROMS RESOLUTION: STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY
Authors
:
K. A. Tiffany, D. L. Roberts, M. Wang, R. Paschke, A. -W. A. Mohsen, J. Vockley, J. J. P. Kim
Date
:
15 May 97 (Deposition) - 20 May 98 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Oxidoreductase, Acyl-Coa Dehydrogenase, Flavoprotein, Isovaleryl-Coa, Isovaleric Acidemia
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. A. Tiffany, D. L. Roberts, M. Wang, R. Paschke, A. W. Mohsen, J. Vockley, J. J. Kim
Structure Of Human Isovaleryl-Coa Dehydrogenase At 2. 6 A Resolution: Structural Basis For Substrate Specificity, .
Biochemistry V. 36 8455 1997
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 8)
Info
All Hetero Components
1a: COENZYME A PERSULFIDE (COSa)
1b: COENZYME A PERSULFIDE (COSb)
1c: COENZYME A PERSULFIDE (COSc)
1d: COENZYME A PERSULFIDE (COSd)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
2d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
COS
4
Ligand/Ion
COENZYME A PERSULFIDE
2
FAD
4
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU A:133 , MET A:135 , SER A:136 , GLY A:141 , SER A:142 , TRP A:166 , THR A:168 , ILE A:373 , THR A:377 , GLU A:379 , LEU A:383 , COS A:400 , HOH A:512 , HOH A:589 , ARG B:280 , PHE B:283 , ILE B:287 , PHE B:290 , MET B:293 , GLN B:348 , CYS B:349 , GLY B:352 , GLN D:291
BINDING SITE FOR RESIDUE FAD A 399
2
AC2
SOFTWARE
GLY A:141 , SER A:142 , VAL A:144 , SER A:190 , ARG A:191 , VAL A:244 , TYR A:245 , MET A:248 , ASP A:252 , GLU A:254 , ARG A:255 , ALA A:375 , GLY A:376 , VAL A:380 , VAL A:384 , ARG A:387 , FAD A:399 , PHE B:283
BINDING SITE FOR RESIDUE COS A 400
3
AC3
SOFTWARE
ARG A:280 , PHE A:283 , PHE A:290 , MET A:293 , GLN A:348 , CYS A:349 , GLY A:352 , LEU B:133 , MET B:135 , SER B:136 , GLY B:141 , SER B:142 , TRP B:166 , ILE B:167 , THR B:168 , LEU B:370 , ILE B:373 , THR B:377 , GLU B:379 , COS B:400 , HOH B:525 , HOH B:531 , HOH B:591 , GLN C:291
BINDING SITE FOR RESIDUE FAD B 399
4
AC4
SOFTWARE
PHE A:283 , GLY B:141 , SER B:142 , VAL B:144 , VAL B:145 , SER B:190 , ARG B:191 , VAL B:244 , TYR B:245 , MET B:248 , LEU B:251 , ASP B:252 , GLU B:254 , ARG B:255 , GLY B:374 , ALA B:375 , GLY B:376 , VAL B:380 , ARG B:387 , FAD B:399 , HOH B:545
BINDING SITE FOR RESIDUE COS B 400
5
AC5
SOFTWARE
GLN B:291 , LEU C:133 , MET C:135 , SER C:136 , GLY C:141 , SER C:142 , TRP C:166 , ILE C:167 , THR C:168 , LEU C:370 , ILE C:373 , THR C:377 , GLU C:379 , LEU C:383 , COS C:400 , HOH C:500 , HOH C:505 , HOH C:517 , HOH C:547 , HOH C:587 , ARG D:280 , PHE D:283 , ILE D:287 , PHE D:290 , MET D:293 , GLN D:348 , CYS D:349 , GLY D:352
BINDING SITE FOR RESIDUE FAD C 399
6
AC6
SOFTWARE
MET C:135 , GLY C:141 , SER C:142 , VAL C:144 , VAL C:145 , SER C:190 , ARG C:191 , VAL C:244 , TYR C:245 , MET C:248 , LEU C:251 , GLU C:254 , ARG C:255 , ALA C:375 , GLY C:376 , VAL C:380 , ARG C:387 , FAD C:399 , HOH C:587 , HOH C:686 , PHE D:283
BINDING SITE FOR RESIDUE COS C 400
7
AC7
SOFTWARE
GLN A:291 , ARG C:280 , ILE C:287 , PHE C:290 , MET C:293 , GLN C:348 , CYS C:349 , GLY C:352 , HOH C:529 , LEU D:133 , MET D:135 , SER D:136 , GLY D:141 , SER D:142 , TRP D:166 , ILE D:167 , THR D:168 , LYS D:213 , LEU D:370 , ILE D:373 , THR D:377 , GLU D:379 , COS D:400 , HOH D:564 , HOH D:605 , HOH D:655
BINDING SITE FOR RESIDUE FAD D 399
8
AC8
SOFTWARE
PHE C:283 , MET D:135 , GLY D:141 , SER D:142 , SER D:190 , VAL D:244 , MET D:248 , LEU D:251 , GLU D:254 , ARG D:255 , GLY D:374 , ALA D:375 , GLY D:376 , VAL D:380 , VAL D:384 , ARG D:387 , FAD D:399
BINDING SITE FOR RESIDUE COS D 400
[
close Site info
]
SAPs(SNPs)/Variants
(14, 56)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_000423 (L13P, chain A/B/C/D, )
02: VAR_015960 (R21P, chain A/B/C/D, )
03: VAR_015961 (D40N, chain A/B/C/D, )
04: VAR_070061 (A65G, chain A/B/C/D, )
05: VAR_070062 (G91R, chain A/B/C/D, )
06: VAR_070063 (I167M, chain A/B/C/D, )
07: VAR_000424 (G170V, chain A/B/C/D, )
08: VAR_070064 (L247P, chain A/B/C/D, )
09: VAR_015962 (A282V, chain A/B/C/D, )
10: VAR_015963 (C328R, chain A/B/C/D, )
11: VAR_015964 (V342A, chain A/B/C/D, )
12: VAR_015965 (R363C, chain A/B/C/D, )
13: VAR_070065 (Y371C, chain A/B/C/D, )
14: VAR_015966 (R382L, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_000423
L
42
P
IVD_HUMAN
Disease (IVA)
---
A/B/C/D
L
13
P
02
UniProt
VAR_015960
R
50
P
IVD_HUMAN
Disease (IVA)
---
A/B/C/D
R
21
P
03
UniProt
VAR_015961
D
69
N
IVD_HUMAN
Disease (IVA)
---
A/B/C/D
D
40
N
04
UniProt
VAR_070061
A
94
G
IVD_HUMAN
Disease (IVA)
---
A/B/C/D
A
65
G
05
UniProt
VAR_070062
G
120
R
IVD_HUMAN
Disease (IVA)
142761835
A/B/C/D
G
91
R
06
UniProt
VAR_070063
I
196
M
IVD_HUMAN
Disease (IVA)
---
A/B/C/D
I
167
M
07
UniProt
VAR_000424
G
199
V
IVD_HUMAN
Disease (IVA)
---
A/B/C/D
G
170
V
08
UniProt
VAR_070064
L
276
P
IVD_HUMAN
Disease (IVA)
---
A/B/C/D
L
247
P
09
UniProt
VAR_015962
A
311
V
IVD_HUMAN
Disease (IVA)
28940889
A/B/C/D
A
282
V
10
UniProt
VAR_015963
C
357
R
IVD_HUMAN
Disease (IVA)
---
A/B/C/D
C
328
R
11
UniProt
VAR_015964
V
371
A
IVD_HUMAN
Disease (IVA)
---
A/B/C/D
V
342
A
12
UniProt
VAR_015965
R
392
C
IVD_HUMAN
Disease (IVA)
---
A/B/C/D
R
363
C
13
UniProt
VAR_070065
Y
400
C
IVD_HUMAN
Disease (IVA)
---
A/B/C/D
Y
371
C
14
UniProt
VAR_015966
R
411
L
IVD_HUMAN
Disease (IVA)
---
A/B/C/D
R
382
L
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 (A:134-146,B:134-146,C:134-146,D:13...)
2: ACYL_COA_DH_2 (A:348-367,B:348-367,C:348-367,D:34...)
;
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.
IVD_HUMAN
163-175
4
A:134-146
B:134-146
C:134-146
D:134-146
2
ACYL_COA_DH_2
PS00073
Acyl-CoA dehydrogenases signature 2.
IVD_HUMAN
377-396
4
A:348-367
B:348-367
C:348-367
D:348-367
[
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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1ivha1 (A:242-392)
1b: SCOP_d1ivhb1 (B:242-392)
1c: SCOP_d1ivhc1 (C:242-392)
1d: SCOP_d1ivhd1 (D:242-392)
2a: SCOP_d1ivha2 (A:6-241)
2b: SCOP_d1ivhb2 (B:6-241)
2c: SCOP_d1ivhc2 (C:6-241)
2d: SCOP_d1ivhd2 (D:6-241)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Bromodomain-like
(339)
Superfamily
:
Acyl-CoA dehydrogenase C-terminal domain-like
(61)
Family
:
Medium chain acyl-CoA dehydrogenase-like, C-terminal domain
(29)
Protein domain
:
Isovaleryl-CoA dehydrogenase, C-domain
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1ivha1
A:242-392
1b
d1ivhb1
B:242-392
1c
d1ivhc1
C:242-392
1d
d1ivhd1
D:242-392
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
:
Isovaleryl-coa dehydrogenase, NM domains
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d1ivha2
A:6-241
2b
d1ivhb2
B:6-241
2c
d1ivhc2
C:6-241
2d
d1ivhd2
D:6-241
[
close SCOP info
]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1ivhA01 (A:9-130)
1b: CATH_1ivhB01 (B:9-130)
1c: CATH_1ivhC01 (C:9-130)
1d: CATH_1ivhD01 (D:9-130)
2a: CATH_1ivhA03 (A:251-391)
2b: CATH_1ivhB03 (B:251-391)
2c: CATH_1ivhC03 (C:251-391)
2d: CATH_1ivhD03 (D:251-391)
3a: CATH_1ivhA02 (A:131-250)
3b: CATH_1ivhB02 (B:131-250)
3c: CATH_1ivhC02 (C:131-250)
3d: CATH_1ivhD02 (D:131-250)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
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
1ivhA01
A:9-130
1b
1ivhB01
B:9-130
1c
1ivhC01
C:9-130
1d
1ivhD01
D:9-130
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
1ivhA03
A:251-391
2b
1ivhB03
B:251-391
2c
1ivhC03
C:251-391
2d
1ivhD03
D:251-391
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
1ivhA02
A:131-250
3b
1ivhB02
B:131-250
3c
1ivhC02
C:131-250
3d
1ivhD02
D:131-250
[
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
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 (258 KB)
Header - Asym.Unit
Biol.Unit 1 (250 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
1IVH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help