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2VLE
Biol. Unit 1
Info
Asym.Unit (1.2 MB)
Biol.Unit 1 (641 KB)
Biol.Unit 2 (636 KB)
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(1)
Title
:
THE STRUCTURE OF DAIDZIN, A NATURALLY OCCURRING ANTI ALCOHOL-ADDICTION AGENT, IN COMPLEX WITH HUMAN MITOCHONDRIAL ALDEHYDE DEHYDROGENASE
Authors
:
E. D. Lowe, G. Y. Gao, L. N. Johnson, W. M. Keung
Date
:
13 Jan 08 (Deposition) - 19 Aug 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Transit Peptide, Aldehyde Dehydrogenase, Nad, Daidzin, Acetylation, Polymorphism, Mitochondrion, Alcohol Abuse, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
E. D. Lowe, G. Y. Gao, L. N. Johnson, W. M. Keung
Structure Of Daidzin, A Naturally Occurring Anti- Alcohol-Addiction Agent, In Complex With Human Mitochondrial Aldehyde Dehydrogenase.
J. Med. Chem. V. 51 4482 2008
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: DAIDZIN (DZNa)
1b: DAIDZIN (DZNb)
1c: DAIDZIN (DZNc)
1d: DAIDZIN (DZNd)
1e: DAIDZIN (DZNe)
1f: DAIDZIN (DZNf)
1g: DAIDZIN (DZNg)
1h: DAIDZIN (DZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DZN
4
Ligand/Ion
DAIDZIN
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
MET A:124 , PHE A:170 , MET A:174 , TRP A:177 , THR A:244 , PHE A:292 , PHE A:296 , CYS A:301 , CYS A:302 , CYS A:303 , ASP A:457 , VAL A:458 , PHE A:459 , HOH A:2198
BINDING SITE FOR RESIDUE DZN A1501
2
AC2
SOFTWARE
MET B:124 , LEU B:173 , MET B:174 , TRP B:177 , THR B:244 , PHE B:292 , PHE B:296 , CYS B:301 , CYS B:303 , ASP B:457 , VAL B:458 , PHE B:459 , HOH B:2100
BINDING SITE FOR RESIDUE DZN B1501
3
AC3
SOFTWARE
MET C:124 , PHE C:170 , LEU C:173 , MET C:174 , TRP C:177 , THR C:244 , PHE C:292 , PHE C:296 , CYS C:301 , CYS C:302 , CYS C:303 , ASP C:457 , VAL C:458 , PHE C:459
BINDING SITE FOR RESIDUE DZN C1501
4
AC4
SOFTWARE
VAL D:120 , PHE D:170 , MET D:174 , TRP D:177 , THR D:244 , PHE D:292 , PHE D:296 , CYS D:301 , CYS D:302 , CYS D:303 , ASP D:457 , VAL D:458 , PHE D:459 , HOH D:2177
BINDING SITE FOR RESIDUE DZN D1501
[
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SAPs(SNPs)/Variants
(3, 12)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_011869 (E320V, chain A/B/C/D, )
2: VAR_011302 (E479K, chain A/B/C/D, )
3: VAR_002248 (E487K, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_011869
E
337
V
ALDH2_HUMAN
Polymorphism
1062136
A/B/C/D
E
320
V
2
UniProt
VAR_011302
E
496
K
ALDH2_HUMAN
Polymorphism
---
A/B/C/D
E
479
K
3
UniProt
VAR_002248
E
504
K
ALDH2_HUMAN
Polymorphism
671
A/B/C/D
E
487
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: ALDEHYDE_DEHYDR_GLU (A:267-274,B:267-274,C:267-274,D:26...)
2: ALDEHYDE_DEHYDR_CYS (A:295-306,B:295-306,C:295-306,D:29...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ALDEHYDE_DEHYDR_GLU
PS00687
Aldehyde dehydrogenases glutamic acid active site.
ALDH2_HUMAN
284-291
4
A:267-274
B:267-274
C:267-274
D:267-274
-
-
-
-
2
ALDEHYDE_DEHYDR_CYS
PS00070
Aldehyde dehydrogenases cysteine active site.
ALDH2_HUMAN
312-323
4
A:295-306
B:295-306
C:295-306
D:295-306
-
-
-
-
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Exons
(0, 0)
Info
All Exons
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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
(1, 8)
Info
All SCOP Domains
1a: SCOP_d2vlea_ (A:)
1b: SCOP_d2vlec_ (C:)
1c: SCOP_d2vled_ (D:)
1d: SCOP_d2vlee_ (E:)
1e: SCOP_d2vlef_ (F:)
1f: SCOP_d2vleg_ (G:)
1g: SCOP_d2vleh_ (H:)
1h: SCOP_d2vleb_ (B:)
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)
Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
ALDH-like
(168)
Superfamily
:
ALDH-like
(168)
Family
:
ALDH-like
(76)
Protein domain
:
automated matches
(24)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d2vlea_
A:
1b
d2vlec_
C:
1c
d2vled_
D:
1d
d2vlee_
E:
1e
d2vlef_
F:
1f
d2vleg_
G:
1g
d2vleh_
H:
1h
d2vleb_
B:
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CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_2vleA01 (A:8-270,A:461-500)
1b: CATH_2vleB01 (B:8-270,B:461-500)
1c: CATH_2vleC01 (C:8-270,C:461-500)
1d: CATH_2vleD01 (D:8-270,D:461-500)
1e: CATH_2vleE01 (E:8-270,E:461-500)
1f: CATH_2vleF01 (F:8-270,F:461-500)
1g: CATH_2vleG01 (G:8-270,G:461-500)
1h: CATH_2vleH01 (H:8-270,H:461-500)
2a: CATH_2vleA02 (A:271-460)
2b: CATH_2vleB02 (B:271-460)
2c: CATH_2vleC02 (C:271-460)
2d: CATH_2vleD02 (D:271-460)
2e: CATH_2vleE02 (E:271-460)
2f: CATH_2vleF02 (F:271-460)
2g: CATH_2vleG02 (G:271-460)
2h: CATH_2vleH02 (H:271-460)
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)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aldehyde Dehydrogenase; Chain A, domain 1
(86)
Homologous Superfamily
:
Aldehyde Dehydrogenase; Chain A, domain 1
(86)
Human (Homo sapiens)
(22)
1a
2vleA01
A:8-270,A:461-500
1b
2vleB01
B:8-270,B:461-500
1c
2vleC01
C:8-270,C:461-500
1d
2vleD01
D:8-270,D:461-500
1e
2vleE01
E:8-270,E:461-500
1f
2vleF01
F:8-270,F:461-500
1g
2vleG01
G:8-270,G:461-500
1h
2vleH01
H:8-270,H:461-500
Topology
:
Aldehyde Dehydrogenase; Chain A, domain 2
(89)
Homologous Superfamily
:
Aldehyde Dehydrogenase; Chain A, domain 2
(89)
Human (Homo sapiens)
(22)
2a
2vleA02
A:271-460
2b
2vleB02
B:271-460
2c
2vleC02
C:271-460
2d
2vleD02
D:271-460
2e
2vleE02
E:271-460
2f
2vleF02
F:271-460
2g
2vleG02
G:271-460
2h
2vleH02
H:271-460
[
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Aldedh_2vleH01 (H:28-491)
1b: PFAM_Aldedh_2vleH02 (H:28-491)
1c: PFAM_Aldedh_2vleH03 (H:28-491)
1d: PFAM_Aldedh_2vleH04 (H:28-491)
1e: PFAM_Aldedh_2vleH05 (H:28-491)
1f: PFAM_Aldedh_2vleH06 (H:28-491)
1g: PFAM_Aldedh_2vleH07 (H:28-491)
1h: PFAM_Aldedh_2vleH08 (H:28-491)
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Clans
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(
)
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(
)
Organisms
(
)
(
)
Clan
:
ALDH-like
(49)
Family
:
Aldedh
(45)
Homo sapiens (Human)
(21)
1a
Aldedh-2vleH01
H:28-491
1b
Aldedh-2vleH02
H:28-491
1c
Aldedh-2vleH03
H:28-491
1d
Aldedh-2vleH04
H:28-491
1e
Aldedh-2vleH05
H:28-491
1f
Aldedh-2vleH06
H:28-491
1g
Aldedh-2vleH07
H:28-491
1h
Aldedh-2vleH08
H:28-491
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