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2HDH
Asym. Unit
Info
Asym.Unit (105 KB)
Biol.Unit 1 (99 KB)
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(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
:
04 Dec 98 (Deposition) - 12 May 99 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
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
)
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Hetero Components
(2, 16)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
1i: SELENOMETHIONINE (MSEi)
1j: SELENOMETHIONINE (MSEj)
1k: SELENOMETHIONINE (MSEk)
1l: SELENOMETHIONINE (MSEl)
1m: SELENOMETHIONINE (MSEm)
1n: SELENOMETHIONINE (MSEn)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
14
Mod. Amino Acid
SELENOMETHIONINE
2
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AS (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:24 , LEU A:25 , MSE A:26 , ASP A:45 , GLN A:46 , ALA A:107 , ILE A:108 , GLU A:110 , LYS A:115 , ASN A:135 , THR A:136 , SER A:137 , HIS A:158 , PHE A:159 , HOH A:802 , HOH A:856 , HOH A:888
BINDING SITE FOR RESIDUE NAD A 350
2
AC2
SOFTWARE
ILE B:21 , GLY B:24 , LEU B:25 , MSE B:26 , ASP B:45 , GLN B:46 , ILE B:50 , ALA B:107 , ILE B:108 , GLU B:110 , LYS B:115 , ASN B:135 , THR B:136 , SER B:137 , HOH B:961 , HOH B:990 , HOH B:1020
BINDING SITE FOR RESIDUE NAD B 750
3
AS
AUTHOR
GLU A:170
ACTIVE SITE RESIDUES
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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)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: 3HCDH (A:201-225,B:201-225)
;
View:
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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
[
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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:
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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
[
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SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2hdha1 (A:204-304)
1b: SCOP_d2hdhb1 (B:204-302)
2a: SCOP_d2hdha2 (A:12-203)
2b: SCOP_d2hdhb2 (B:12-203)
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Protein Domains
(
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(
)
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
d2hdha1
A:204-304
1b
d2hdhb1
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
d2hdha2
A:12-203
2b
d2hdhb2
B:12-203
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2hdhA01 (A:12-207)
1b: CATH_2hdhB01 (B:12-207)
2a: CATH_2hdhA02 (A:211-303)
2b: CATH_2hdhB02 (B:211-295)
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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
2hdhA01
A:12-207
1b
2hdhB01
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
2hdhA02
A:211-303
2b
2hdhB02
B:211-295
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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