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3SZ9
Biol. Unit 3
Info
Asym.Unit (677 KB)
Biol.Unit 1 (173 KB)
Biol.Unit 2 (175 KB)
Biol.Unit 3 (178 KB)
Biol.Unit 4 (175 KB)
Biol.Unit 5 (337 KB)
Biol.Unit 6 (342 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN ALDH2 MODIFIED WITH THE BETA-ELIMINATION PRODUCT OF ALDI-3; 1-(4-ETHYLBENZENE)PROP-2-EN-1-ONE
Authors
:
S. Perez-Miller, T. D. Hurley
Date
:
18 Jul 11 (Deposition) - 02 Nov 11 (Release) - 28 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Biol. Unit 5: A,B,C,D (1x)
Biol. Unit 6: E,F,G,H (1x)
Keywords
:
Aldh, Aldi-3, Inhibitor, Rossmann Fold, Oxidoreductase, Covalent Adduct, Mitochondria, Oxidoreductase-Oxidoreductase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Khanna, C. H. Chen, A. Kimble-Hill, B. Parajuli, S. Perez-Miller, S. Baskaran, J. Kim, K. Dria, V. Vasiliou, D. Mochly-Rosen, T. D. Hurle
Discovery Of A Novel Class Of Covalent Inhibitor For Aldehyde Dehydrogenases.
J. Biol. Chem. V. 286 43486 2011
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 15)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
1m: 1,2-ETHANEDIOL (EDOm)
1n: 1,2-ETHANEDIOL (EDOn)
1o: 1,2-ETHANEDIOL (EDOo)
1p: 1,2-ETHANEDIOL (EDOp)
1q: 1,2-ETHANEDIOL (EDOq)
1r: 1,2-ETHANEDIOL (EDOr)
1s: 1,2-ETHANEDIOL (EDOs)
1t: 1,2-ETHANEDIOL (EDOt)
1u: 1,2-ETHANEDIOL (EDOu)
2a: GUANIDINE (GAIa)
2b: GUANIDINE (GAIb)
2c: GUANIDINE (GAIc)
2d: GUANIDINE (GAId)
2e: GUANIDINE (GAIe)
2f: GUANIDINE (GAIf)
2g: GUANIDINE (GAIg)
2h: GUANIDINE (GAIh)
2i: GUANIDINE (GAIi)
2j: GUANIDINE (GAIj)
2k: GUANIDINE (GAIk)
2l: GUANIDINE (GAIl)
2m: GUANIDINE (GAIm)
2n: GUANIDINE (GAIn)
2o: GUANIDINE (GAIo)
2p: GUANIDINE (GAIp)
2q: GUANIDINE (GAIq)
2r: GUANIDINE (GAIr)
3a: 1-(4-ETHYLPHENYL)PROPAN-1-ONE (I3Ea)
3b: 1-(4-ETHYLPHENYL)PROPAN-1-ONE (I3Eb)
3c: 1-(4-ETHYLPHENYL)PROPAN-1-ONE (I3Ec)
3d: 1-(4-ETHYLPHENYL)PROPAN-1-ONE (I3Ed)
3e: 1-(4-ETHYLPHENYL)PROPAN-1-ONE (I3Ee)
3f: 1-(4-ETHYLPHENYL)PROPAN-1-ONE (I3Ef)
3g: 1-(4-ETHYLPHENYL)PROPAN-1-ONE (I3Eg)
3h: 1-(4-ETHYLPHENYL)PROPAN-1-ONE (I3Eh)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
4e: SODIUM ION (NAe)
4f: SODIUM ION (NAf)
4g: SODIUM ION (NAg)
4h: SODIUM ION (NAh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
8
Ligand/Ion
1,2-ETHANEDIOL
2
GAI
5
Ligand/Ion
GUANIDINE
3
I3E
2
Ligand/Ion
1-(4-ETHYLPHENYL)PROPAN-1-ONE
4
NA
-1
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(20, 20)
Info
All Sites
01: CC2 (SOFTWARE)
02: CC9 (SOFTWARE)
03: DC1 (SOFTWARE)
04: DC2 (SOFTWARE)
05: DC3 (SOFTWARE)
06: DC4 (SOFTWARE)
07: DC5 (SOFTWARE)
08: DC6 (SOFTWARE)
09: DC7 (SOFTWARE)
10: DC8 (SOFTWARE)
11: DC9 (SOFTWARE)
12: EC1 (SOFTWARE)
13: EC2 (SOFTWARE)
14: EC3 (SOFTWARE)
15: EC4 (SOFTWARE)
16: EC5 (SOFTWARE)
17: EC6 (SOFTWARE)
18: EC7 (SOFTWARE)
19: FC7 (SOFTWARE)
20: FC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
CC2
SOFTWARE
GLU C:347 , GAI C:6821 , GLY F:45
BINDING SITE FOR RESIDUE EDO C 6961
02
CC9
SOFTWARE
THR E:39 , VAL E:40 , ASP E:109 , GLN E:196 , HOH E:2549
BINDING SITE FOR RESIDUE NA E 601
03
DC1
SOFTWARE
PHE E:70 , GLU E:157 , PRO E:158 , VAL E:159 , HOH E:1588 , TYR F:468
BINDING SITE FOR RESIDUE GAI E 6801
04
DC2
SOFTWARE
TYR E:153 , ARG E:155 , SER F:443 , PHE H:151
BINDING SITE FOR RESIDUE EDO E 6901
05
DC3
SOFTWARE
PHE E:18 , TYR E:101 , TYR E:203 , HOH E:2283
BINDING SITE FOR RESIDUE EDO E 6921
06
DC4
SOFTWARE
PHE E:170 , GLU E:268 , PHE E:296 , CYS E:301 , CYS E:302 , PHE E:459
BINDING SITE FOR RESIDUE I3E E 8001
07
DC5
SOFTWARE
PHE E:459 , ILE F:146 , ASP F:147 , PHE F:150
BINDING SITE FOR RESIDUE GAI E 6811
08
DC6
SOFTWARE
ASP E:147 , PHE E:150 , PHE F:459 , HOH F:1930
BINDING SITE FOR RESIDUE GAI F 6811
09
DC7
SOFTWARE
THR F:39 , VAL F:40 , ASP F:109 , GLN F:196 , HOH F:591
BINDING SITE FOR RESIDUE NA F 601
10
DC8
SOFTWARE
TYR E:468 , GLU F:157 , PRO F:158 , VAL F:159 , HOH F:549 , HOH F:1128 , HOH F:2342
BINDING SITE FOR RESIDUE GAI F 6801
11
DC9
SOFTWARE
ALA F:375 , ASP F:376 , GLY F:378 , HOH F:2564 , EDO F:6961
BINDING SITE FOR RESIDUE GAI F 6821
12
EC1
SOFTWARE
SER E:443 , TYR F:153 , ARG F:155 , PHE G:151
BINDING SITE FOR RESIDUE EDO F 6901
13
EC2
SOFTWARE
ASN F:41 , THR F:44 , GLU F:46 , LEU F:108 , HOH F:2374
BINDING SITE FOR RESIDUE EDO F 6911
14
EC3
SOFTWARE
PHE F:18 , TYR F:101 , TYR F:203 , HOH F:629 , HOH F:1304 , HOH F:2251
BINDING SITE FOR RESIDUE EDO F 6921
15
EC4
SOFTWARE
ILE B:373 , ALA F:68 , SER F:74 , HOH F:617 , HOH F:2184
BINDING SITE FOR RESIDUE EDO F 6951
16
EC5
SOFTWARE
GLY C:45 , GLU F:347 , GAI F:6821
BINDING SITE FOR RESIDUE EDO F 6961
17
EC6
SOFTWARE
ASN F:169 , PHE F:170 , GLU F:268 , PHE F:296 , CYS F:301 , CYS F:302 , PHE F:459
BINDING SITE FOR RESIDUE I3E F 8001
18
EC7
SOFTWARE
PHE F:151 , TYR G:153 , ARG G:155 , SER H:443
BINDING SITE FOR RESIDUE EDO F 501
19
FC7
SOFTWARE
PHE E:151 , SER G:443 , TYR H:153 , ARG H:155
BINDING SITE FOR RESIDUE EDO H 6901
20
FC9
SOFTWARE
LYS E:361 , PHE H:18 , TYR H:101 , TYR H:203
BINDING SITE FOR RESIDUE EDO H 6921
[
close Site info
]
SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_011869 (E320V, chain E/F, )
2: VAR_011302 (E479K, chain E/F, )
3: VAR_002248 (E487K, chain E/F, )
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
E/F
E
320
V
2
UniProt
VAR_011302
E
496
K
ALDH2_HUMAN
Polymorphism
---
E/F
E
479
K
3
UniProt
VAR_002248
E
504
K
ALDH2_HUMAN
Polymorphism
671
E/F
E
487
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: ALDEHYDE_DEHYDR_GLU (E:267-274,F:267-274)
2: ALDEHYDE_DEHYDR_CYS (E:295-306,F:295-306)
;
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
2
-
-
-
-
E:267-274
F:267-274
-
-
2
ALDEHYDE_DEHYDR_CYS
PS00070
Aldehyde dehydrogenases cysteine active site.
ALDH2_HUMAN
312-323
2
-
-
-
-
E:295-306
F:295-306
-
-
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
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_d3sz9a_ (A:)
1b: SCOP_d3sz9b_ (B:)
1c: SCOP_d3sz9c_ (C:)
1d: SCOP_d3sz9d_ (D:)
1e: SCOP_d3sz9e_ (E:)
1f: SCOP_d3sz9f_ (F:)
1g: SCOP_d3sz9g_ (G:)
1h: SCOP_d3sz9h_ (H:)
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(
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(
)
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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
:
Aldehyde reductase (dehydrogenase), ALDH
(39)
Human (Homo sapiens), mitochondrial [TaxId: 9606]
(25)
1a
d3sz9a_
A:
1b
d3sz9b_
B:
1c
d3sz9c_
C:
1d
d3sz9d_
D:
1e
d3sz9e_
E:
1f
d3sz9f_
F:
1g
d3sz9g_
G:
1h
d3sz9h_
H:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
[
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Asymmetric Unit 1
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Asym.Unit (677 KB)
Header - Asym.Unit
Biol.Unit 1 (173 KB)
Header - Biol.Unit 1
Biol.Unit 2 (175 KB)
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Biol.Unit 3 (178 KB)
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Biol.Unit 4 (175 KB)
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Biol.Unit 5 (337 KB)
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