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.
3HAD
Asym. Unit
Info
Asym.Unit (106 KB)
Biol.Unit 1 (101 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
BIOCHEMICAL CHARACTERIZATION AND STRUCTURE DETERMINATION OF HUMAN HEART SHORT CHAIN L-3-HYDROXYACYL COA DEHYDROGENASE PROVIDE INSIGHT INTO CATALYTIC MECHANISM
Authors
:
J. J. Barycki, J. M. Bratt, L. J. Banaszak
Date
:
03 Dec 98 (Deposition) - 12 Jan 00 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Oxidoreductase, Beta Oxidation, Schad, Catalytic Activity: L-3- Hydroxyacyl-Coa + Nad(+) = 3-Oxoacyl-Coa + Nadh
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. J. Barycki, L. K. O'Brien, J. M. Bratt, R. Zhang, R. Sanishvili, A. W. Strauss, L. J. Banaszak
Biochemical Characterization And Crystal Structure Determination Of Human Heart Short Chain L-3-Hydroxyacyl-Co Dehydrogenase Provide Insights Into Catalytic Mechanism.
Biochemistry V. 38 5786 1999
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: ASA (AUTHOR)
4: ASB (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:24 , LEU A:25 , MET A:26 , ASP A:45 , GLN A:46 , ALA A:107 , ILE A:108 , VAL A:109 , GLU A:110 , LYS A:115 , ASN A:135 , THR A:136 , SER A:137 , HIS A:158 , PHE A:159 , HOH A:836 , HOH A:901 , HOH A:929 , HOH A:1002 , HOH A:1016 , HOH A:1045 , HOH A:1047 , HOH A:1067 , HOH A:1080
BINDING SITE FOR RESIDUE NAD A 350
2
AC2
SOFTWARE
GLY B:22 , GLY B:24 , LEU B:25 , MET B:26 , ASP B:45 , GLN B:46 , ALA B:107 , ILE B:108 , VAL B:109 , GLU B:110 , LYS B:115 , ASN B:135 , THR B:136 , SER B:137 , HIS B:158 , PHE B:159 , HOH B:1093
BINDING SITE FOR RESIDUE NAD B 750
3
ASA
AUTHOR
HIS A:158 , GLU A:170
ACTIVE SITE RESIDUES
4
ASB
AUTHOR
HIS B:158 , GLU B:170
ACTIVE SITE RESIDUES
[
close Site info
]
SAPs(SNPs)/Variants
(5, 10)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_024079 (A28T, chain A/B, )
2: VAR_024080 (D45E, chain A/B, )
3: VAR_026764 (P74P, chain A/B, )
4: VAR_055701 (Q140H, chain A/B, )
5: VAR_024081 (P246L, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_024079
A
40
T
HCDH_HUMAN
Disease (HADH deficiency)
---
A/B
A
28
T
2
UniProt
VAR_024080
D
57
E
HCDH_HUMAN
Disease (HADH deficiency)
---
A/B
D
45
E
3
UniProt
VAR_026764
L
86
P
HCDH_HUMAN
Polymorphism
4956145
A/B
P
74
P
4
UniProt
VAR_055701
Q
152
H
HCDH_HUMAN
Polymorphism
1051519
A/B
Q
140
H
5
UniProt
VAR_024081
P
258
L
HCDH_HUMAN
Disease (HHF4)
---
A/B
P
246
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: 3HCDH (A:201-225,B:201-225)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
3HCDH
PS00067
3-hydroxyacyl-CoA dehydrogenase signature.
HCDH_HUMAN
213-237
2
A:201-225
B:201-225
[
close PROSITE info
]
Exons
(8, 16)
Info
All Exons
Exon 1.1c (A:12-32 | B:12-32)
Exon 1.4 (A:33-75 | B:33-75)
Exon 1.5a (A:76-128 | B:76-128)
Exon 1.6 (A:128-170 | B:128-170)
Exon 1.7 (A:171-200 | B:171-200)
Exon 1.8b (A:201-225 | B:201-225)
Exon 1.10b (A:225-264 | B:225-264)
Exon 1.11d (A:264-302 | B:264-302)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1c
2: Boundary 1.1c/1.4
3: Boundary 1.4/1.5a
4: Boundary 1.5a/1.6
5: Boundary 1.6/1.7
6: Boundary 1.7/1.8b
7: Boundary 1.8b/1.10b
8: Boundary 1.10b/1.11d
9: Boundary 1.11d/-
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
1.1c
ENST00000309522
1c
ENSE00001196027
chr4:
108910940-108911220
281
HCDH_HUMAN
1-44
44
2
A:12-32
B:12-32
21
21
1.4
ENST00000309522
4
ENSE00000333879
chr4:
108930915-108931043
129
HCDH_HUMAN
45-87
43
2
A:33-75
B:33-75
43
43
1.5a
ENST00000309522
5a
ENSE00000841666
chr4:
108935587-108935744
158
HCDH_HUMAN
88-140
53
2
A:76-128
B:76-128
53
53
1.6
ENST00000309522
6
ENSE00000841667
chr4:
108940696-108940822
127
HCDH_HUMAN
140-182
43
2
A:128-170
B:128-170
43
43
1.7
ENST00000309522
7
ENSE00000841668
chr4:
108944630-108944719
90
HCDH_HUMAN
183-212
30
2
A:171-200
B:171-200
30
30
1.8b
ENST00000309522
8b
ENSE00000841669
chr4:
108948844-108948916
73
HCDH_HUMAN
213-237
25
2
A:201-225
B:201-225
25
25
1.10b
ENST00000309522
10b
ENSE00000841670
chr4:
108954332-108954448
117
HCDH_HUMAN
237-276
40
2
A:225-264
B:225-264
40
40
1.11d
ENST00000309522
11d
ENSE00001561694
chr4:
108955395-108956331
937
HCDH_HUMAN
276-314
39
2
A:264-302
B:264-302
39
39
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3hada1 (A:204-304)
1b: SCOP_d3hadb1 (B:204-302)
2a: SCOP_d3hada2 (A:12-203)
2b: SCOP_d3hadb2 (B:12-203)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
:
Short chain L-3-hydroxyacyl CoA dehydrogenase
(12)
Human (Homo sapiens) [TaxId: 9606]
(11)
1a
d3hada1
A:204-304
1b
d3hadb1
B:204-302
Class
:
Alpha and beta proteins (a/b)
(23833)
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
:
Short chain L-3-hydroxyacyl CoA dehydrogenase
(12)
Human (Homo sapiens) [TaxId: 9606]
(11)
2a
d3hada2
A:12-203
2b
d3hadb2
B:12-203
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3hadA01 (A:12-207)
1b: CATH_3hadB01 (B:12-207)
2a: CATH_3hadA02 (A:211-297)
2b: CATH_3hadB02 (B:211-297)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
1a
3hadA01
A:12-207
1b
3hadB01
B:12-207
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
(60)
Homologous Superfamily
:
N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
(59)
Human (Homo sapiens)
(12)
2a
3hadA02
A:211-297
2b
3hadB02
B:211-297
[
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
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 (106 KB)
Header - Asym.Unit
Biol.Unit 1 (101 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
3HAD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
