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2VLE
Asym. Unit
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)
]
)
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, 8)
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
8
Ligand/Ion
DAIDZIN
[
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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
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
5
AC5
SOFTWARE
MET E:124 , PHE E:170 , LEU E:173 , MET E:174 , TRP E:177 , THR E:244 , PHE E:292 , PHE E:296 , CYS E:301 , CYS E:302 , CYS E:303 , ASP E:457 , VAL E:458 , PHE E:459 , HOH E:2162
BINDING SITE FOR RESIDUE DZN E1501
6
AC6
SOFTWARE
MET F:124 , PHE F:170 , LEU F:173 , MET F:174 , TRP F:177 , THR F:244 , PHE F:292 , PHE F:296 , CYS F:301 , CYS F:302 , CYS F:303 , ASP F:457 , VAL F:458 , PHE F:459
BINDING SITE FOR RESIDUE DZN F1501
7
AC7
SOFTWARE
MET G:124 , LEU G:173 , MET G:174 , TRP G:177 , THR G:244 , PHE G:292 , PHE G:296 , CYS G:301 , CYS G:303 , ASP G:457 , VAL G:458 , PHE G:459 , HOH G:2076 , HOH G:2089
BINDING SITE FOR RESIDUE DZN G1501
8
AC8
SOFTWARE
MET H:124 , PHE H:170 , MET H:174 , TRP H:177 , THR H:244 , PHE H:292 , PHE H:296 , CYS H:301 , CYS H:302 , CYS H:303 , ASP H:457 , VAL H:458 , PHE H:459 , HOH H:2146 , HOH H:2148
BINDING SITE FOR RESIDUE DZN H1501
[
close Site info
]
SAPs(SNPs)/Variants
(3, 24)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_011869 (E320V, chain A/B/C/D/E/F/G/H, )
2: VAR_011302 (E479K, chain A/B/C/D/E/F/G/H, )
3: VAR_002248 (E487K, chain A/B/C/D/E/F/G/H, )
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/F/G/H
E
320
V
2
UniProt
VAR_011302
E
496
K
ALDH2_HUMAN
Polymorphism
---
A/B/C/D/E/F/G/H
E
479
K
3
UniProt
VAR_002248
E
504
K
ALDH2_HUMAN
Polymorphism
671
A/B/C/D/E/F/G/H
E
487
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 16)
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:
Select:
Label:
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
8
A:267-274
B:267-274
C:267-274
D:267-274
E:267-274
F:267-274
G:267-274
H:267-274
2
ALDEHYDE_DEHYDR_CYS
PS00070
Aldehyde dehydrogenases cysteine active site.
ALDH2_HUMAN
312-323
8
A:295-306
B:295-306
C:295-306
D:295-306
E:295-306
F:295-306
G:295-306
H:295-306
[
close PROSITE info
]
Exons
(13, 104)
Info
All Exons
Exon 1.1 (A:7-21 | B:7-21 | C:7-21 | D:7-21 ...)
Exon 1.2 (A:22-56 | B:22-56 | C:22-56 | D:22...)
Exon 1.3 (A:57-103 | B:57-103 | C:57-103 | D...)
Exon 1.4 (A:104-130 | B:104-130 | C:104-130 ...)
Exon 1.5 (A:130-167 | B:130-167 | C:130-167 ...)
Exon 1.6 (A:168-210 | B:168-210 | C:168-210 ...)
Exon 1.7 (A:211-248 | B:211-248 | C:211-248 ...)
Exon 1.8 (A:249-283 | B:249-283 | C:249-283 ...)
Exon 1.9 (A:283-344 | B:283-344 | C:283-344 ...)
Exon 1.10 (A:345-399 | B:345-399 | C:345-399 ...)
Exon 1.11 (A:400-452 | B:400-452 | C:400-452 ...)
Exon 1.12 (A:452-490 | B:452-490 | C:452-490 ...)
Exon 1.13 (A:491-500 | B:491-500 | C:491-500 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8
09: Boundary 1.8/1.9
10: Boundary 1.9/1.10
11: Boundary 1.10/1.11
12: Boundary 1.11/1.12
13: Boundary 1.12/1.13
14: Boundary 1.13/-
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
1.1
ENST00000261733
1
ENSE00001297894
chr12:
112204346-112204900
555
ALDH2_HUMAN
1-38
38
8
A:7-21
B:7-21
C:7-21
D:7-21
E:7-21
F:7-21
G:7-21
H:7-21
15
15
15
15
15
15
15
15
1.2
ENST00000261733
2
ENSE00001302483
chr12:
112219722-112219826
105
ALDH2_HUMAN
39-73
35
8
A:22-56
B:22-56
C:22-56
D:22-56
E:22-56
F:22-56
G:22-56
H:22-56
35
35
35
35
35
35
35
35
1.3
ENST00000261733
3
ENSE00000755216
chr12:
112220962-112221102
141
ALDH2_HUMAN
74-120
47
8
A:57-103
B:57-103
C:57-103
D:57-103
E:57-103
F:57-103
G:57-103
H:57-103
47
47
47
47
47
47
47
47
1.4
ENST00000261733
4
ENSE00000755217
chr12:
112223071-112223150
80
ALDH2_HUMAN
121-147
27
8
A:104-130
B:104-130
C:104-130
D:104-130
E:104-130
F:104-130
G:104-130
H:104-130
27
27
27
27
27
27
27
27
1.5
ENST00000261733
5
ENSE00000755218
chr12:
112227627-112227738
112
ALDH2_HUMAN
147-184
38
8
A:130-167
B:130-167
C:130-167
D:130-167
E:130-167
F:130-167
G:130-167
H:130-167
38
38
38
38
38
38
38
38
1.6
ENST00000261733
6
ENSE00001316176
chr12:
112228238-112228366
129
ALDH2_HUMAN
185-227
43
8
A:168-210
B:168-210
C:168-210
D:168-210
E:168-210
F:168-210
G:168-210
H:168-210
43
43
43
43
43
43
43
43
1.7
ENST00000261733
7
ENSE00000755220
chr12:
112229110-112229223
114
ALDH2_HUMAN
228-265
38
8
A:211-248
B:211-248
C:211-248
D:211-248
E:211-248
F:211-248
G:211-248
H:211-248
38
38
38
38
38
38
38
38
1.8
ENST00000261733
8
ENSE00000755221
chr12:
112229865-112229967
103
ALDH2_HUMAN
266-300
35
8
A:249-283
B:249-283
C:249-283
D:249-283
E:249-283
F:249-283
G:249-283
H:249-283
35
35
35
35
35
35
35
35
1.9
ENST00000261733
9
ENSE00000755222
chr12:
112230402-112230586
185
ALDH2_HUMAN
300-361
62
8
A:283-344
B:283-344
C:283-344
D:283-344
E:283-344
F:283-344
G:283-344
H:283-344
62
62
62
62
62
62
62
62
1.10
ENST00000261733
10
ENSE00000755223
chr12:
112235882-112236046
165
ALDH2_HUMAN
362-416
55
8
A:345-399
B:345-399
C:345-399
D:345-399
E:345-399
F:345-399
G:345-399
H:345-399
55
55
55
55
55
55
55
55
1.11
ENST00000261733
11
ENSE00000755233
chr12:
112237710-112237867
158
ALDH2_HUMAN
417-469
53
8
A:400-452
B:400-452
C:400-452
D:400-452
E:400-452
F:400-452
G:400-452
H:400-452
53
53
53
53
53
53
53
53
1.12
ENST00000261733
12
ENSE00001304774
chr12:
112241663-112241777
115
ALDH2_HUMAN
469-507
39
8
A:452-490
B:452-490
C:452-490
D:452-490
E:452-490
F:452-490
G:452-490
H:452-490
39
39
39
39
39
39
39
39
1.13
ENST00000261733
13
ENSE00001129780
chr12:
112247347-112247782
436
ALDH2_HUMAN
508-517
10
8
A:491-500
B:491-500
C:491-500
D:491-500
E:491-500
F:491-500
G:491-500
H:491-500
10
10
10
10
10
10
10
10
[
close EXON info
]
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
(
)
(
)
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)
View:
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)
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)
Homologous Superfamilies
(
)
(
)
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
(
)
(
)
Families
(
)
(
)
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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Asym.Unit (1.2 MB)
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Biol.Unit 1 (641 KB)
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