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3INL
Biol. Unit 2
Info
Asym.Unit (690 KB)
Biol.Unit 1 (344 KB)
Biol.Unit 2 (347 KB)
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(1)
Title
:
HUMAN MITOCHONDRIAL ALDEHYDE DEHYDROGENASE ASIAN VARIANT, ALDH2*2, COMPLEXED WITH AGONIST ALDA-1
Authors
:
S. Perez-Miller, T. D. Hurley
Date
:
12 Aug 09 (Deposition) - 12 Jan 10 (Release) - 11 Aug 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.86
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
:
Oxidoreductase, Aldh, E487K, Rossmann Fold, Alda-1, Activator, Mitochondrion, Nad, Transit Peptide
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Perez-Miller, H. Younus, R. Vanam, C. H. Chen, D. Mochly-Rosen, T. D. Hurley
Alda-1 Is An Agonist And Chemical Chaperone For The Common Human Aldehyde Dehydrogenase 2 Variant.
Nat. Struct. Mol. Biol. V. 17 159 2010
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 20)
Info
All Hetero Components
1a: N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6... (BXBa)
1b: N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6... (BXBb)
1c: N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6... (BXBc)
1d: N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6... (BXBd)
1e: N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6... (BXBe)
1f: N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6... (BXBf)
1g: N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6... (BXBg)
1h: N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6... (BXBh)
2a: 1,2-ETHANEDIOL (EDOa)
2aa: 1,2-ETHANEDIOL (EDOaa)
2ab: 1,2-ETHANEDIOL (EDOab)
2ac: 1,2-ETHANEDIOL (EDOac)
2ad: 1,2-ETHANEDIOL (EDOad)
2ae: 1,2-ETHANEDIOL (EDOae)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
2z: 1,2-ETHANEDIOL (EDOz)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
3e: SODIUM ION (NAe)
3f: SODIUM ION (NAf)
3g: SODIUM ION (NAg)
3h: SODIUM ION (NAh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BXB
4
Ligand/Ion
N-(1,3-BENZODIOXOL-5-YLMETHYL)-2,6-DICHLOROBENZAMIDE
2
EDO
16
Ligand/Ion
1,2-ETHANEDIOL
3
NA
-1
Ligand/Ion
SODIUM ION
[
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]
Sites
(24, 24)
Info
All Sites
01: CC6 (SOFTWARE)
02: CC7 (SOFTWARE)
03: CC8 (SOFTWARE)
04: CC9 (SOFTWARE)
05: DC1 (SOFTWARE)
06: DC2 (SOFTWARE)
07: DC3 (SOFTWARE)
08: DC4 (SOFTWARE)
09: DC5 (SOFTWARE)
10: DC6 (SOFTWARE)
11: DC7 (SOFTWARE)
12: DC8 (SOFTWARE)
13: DC9 (SOFTWARE)
14: EC1 (SOFTWARE)
15: EC2 (SOFTWARE)
16: EC3 (SOFTWARE)
17: EC4 (SOFTWARE)
18: EC5 (SOFTWARE)
19: EC6 (SOFTWARE)
20: EC7 (SOFTWARE)
21: EC8 (SOFTWARE)
22: EC9 (SOFTWARE)
23: FC1 (SOFTWARE)
24: FC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
CC6
SOFTWARE
THR E:39 , VAL E:40 , ASP E:109 , GLN E:196 , HOH E:503
BINDING SITE FOR RESIDUE NA E 601
02
CC7
SOFTWARE
ASN E:169 , CYS E:301 , SER E:302 , PHE E:465 , BXB E:1001 , HOH E:2328
BINDING SITE FOR RESIDUE EDO E 701
03
CC8
SOFTWARE
ARG E:329 , VAL E:330 , VAL E:331 , HOH E:2473 , HOH E:2895 , HOH E:3046
BINDING SITE FOR RESIDUE EDO E 702
04
CC9
SOFTWARE
TYR E:153 , ARG E:155 , SER F:443 , PHE H:151
BINDING SITE FOR RESIDUE EDO E 703
05
DC1
SOFTWARE
PHE E:18 , TYR E:101 , TYR E:203 , HOH E:538 , HOH E:1986
BINDING SITE FOR RESIDUE EDO E 704
06
DC2
SOFTWARE
MET E:124 , PHE E:170 , LEU E:173 , PHE E:292 , PHE E:296 , ASP E:457 , VAL E:458 , PHE E:459 , EDO E:701 , HOH E:2027
BINDING SITE FOR RESIDUE BXB E 1001
07
DC3
SOFTWARE
PHE E:151 , SER G:443 , TYR H:153 , ARG H:155
BINDING SITE FOR RESIDUE EDO E 501
08
DC4
SOFTWARE
THR F:39 , VAL F:40 , ASP F:109 , GLN F:196 , HOH F:502
BINDING SITE FOR RESIDUE NA F 601
09
DC5
SOFTWARE
ASN F:169 , PHE F:170 , SER F:302 , CYS F:303 , PHE F:465 , BXB F:1001
BINDING SITE FOR RESIDUE EDO F 701
10
DC6
SOFTWARE
ASN F:41 , THR F:44 , GLU F:46 , HOH F:1546
BINDING SITE FOR RESIDUE EDO F 703
11
DC7
SOFTWARE
MET F:124 , PHE F:170 , LEU F:173 , PHE F:292 , PHE F:296 , ASP F:457 , PHE F:459 , EDO F:701 , HOH F:1400
BINDING SITE FOR RESIDUE BXB F 1001
12
DC8
SOFTWARE
PHE F:151 , TYR G:153 , ARG G:155 , SER H:443
BINDING SITE FOR RESIDUE EDO F 501
13
DC9
SOFTWARE
ASN E:440 , SER E:443 , TYR F:153 , ARG F:155 , PHE G:151
BINDING SITE FOR RESIDUE EDO G 702
14
EC1
SOFTWARE
THR G:39 , VAL G:40 , ASP G:109 , GLN G:196 , HOH G:503
BINDING SITE FOR RESIDUE NA G 601
15
EC2
SOFTWARE
ASN G:169 , SER G:302 , CYS G:303 , PHE G:465 , BXB G:1001
BINDING SITE FOR RESIDUE EDO G 701
16
EC3
SOFTWARE
ILE G:373 , ALA G:375 , ASP G:376 , GLY G:378
BINDING SITE FOR RESIDUE EDO G 501
17
EC4
SOFTWARE
ASN G:41 , THR G:44 , ILE G:48 , LEU G:108
BINDING SITE FOR RESIDUE EDO G 704
18
EC5
SOFTWARE
ASP G:98 , TYR G:101 , TYR G:203 , HOH G:534 , HOH G:951
BINDING SITE FOR RESIDUE EDO G 705
19
EC6
SOFTWARE
MET G:124 , PHE G:170 , LEU G:173 , PHE G:292 , PHE G:296 , ASP G:457 , PHE G:459 , HOH G:591 , EDO G:701 , HOH G:884
BINDING SITE FOR RESIDUE BXB G 1001
20
EC7
SOFTWARE
THR H:39 , VAL H:40 , ASP H:109 , GLN H:196 , HOH H:501
BINDING SITE FOR RESIDUE NA H 601
21
EC8
SOFTWARE
ASN H:169 , PHE H:170 , SER H:302 , CYS H:303 , BXB H:1001
BINDING SITE FOR RESIDUE EDO H 701
22
EC9
SOFTWARE
ASN H:41 , THR H:44 , GLU H:46 , VAL H:47
BINDING SITE FOR RESIDUE EDO H 703
23
FC1
SOFTWARE
PHE H:18 , TYR H:101 , TYR H:203 , HOH H:1808
BINDING SITE FOR RESIDUE EDO H 704
24
FC2
SOFTWARE
MET H:124 , PHE H:170 , LEU H:173 , TRP H:177 , PHE H:292 , PHE H:296 , ASP H:457 , PHE H:459 , EDO H:701 , HOH H:1597
BINDING SITE FOR RESIDUE BXB H 1001
[
close Site info
]
SAPs(SNPs)/Variants
(3, 12)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_011869 (E320V, chain E/F/G/H, )
2: VAR_011302 (E479K, chain E/F/G/H, )
3: VAR_002248 (K487K, chain 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
E/F/G/H
E
320
V
2
UniProt
VAR_011302
E
496
K
ALDH2_HUMAN
Polymorphism
---
E/F/G/H
E
479
K
3
UniProt
VAR_002248
E
504
K
ALDH2_HUMAN
Polymorphism
671
E/F/G/H
K
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 (E:267-274,F:267-274,G:267-274,H:26...)
2: ALDEHYDE_DEHYDR_CYS (E:295-306,F:295-306,G:295-306,H: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
4
-
-
-
-
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
4
-
-
-
-
E:295-306
F:295-306
G:295-306
H:295-306
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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_d3inla_ (A:)
1b: SCOP_d3inlb_ (B:)
1c: SCOP_d3inlc_ (C:)
1d: SCOP_d3inld_ (D:)
1e: SCOP_d3inle_ (E:)
1f: SCOP_d3inlf_ (F:)
1g: SCOP_d3inlg_ (G:)
1h: SCOP_d3inlh_ (H:)
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Classes
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)
(
)
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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
d3inla_
A:
1b
d3inlb_
B:
1c
d3inlc_
C:
1d
d3inld_
D:
1e
d3inle_
E:
1f
d3inlf_
F:
1g
d3inlg_
G:
1h
d3inlh_
H:
[
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]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_3inlA01 (A:8-270,A:461-500)
1b: CATH_3inlB01 (B:8-270,B:461-500)
1c: CATH_3inlC01 (C:8-270,C:461-500)
1d: CATH_3inlD01 (D:8-270,D:461-500)
1e: CATH_3inlE01 (E:8-270,E:461-500)
1f: CATH_3inlF01 (F:8-270,F:461-500)
1g: CATH_3inlG01 (G:8-270,G:461-500)
1h: CATH_3inlH01 (H:8-270,H:461-500)
2a: CATH_3inlA02 (A:271-460)
2b: CATH_3inlC02 (C:271-460)
2c: CATH_3inlD02 (D:271-460)
2d: CATH_3inlE02 (E:271-460)
2e: CATH_3inlF02 (F:271-460)
2f: CATH_3inlG02 (G:271-460)
2g: CATH_3inlH02 (H:271-460)
2h: CATH_3inlB02 (B:271-460)
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Topologies
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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
3inlA01
A:8-270,A:461-500
1b
3inlB01
B:8-270,B:461-500
1c
3inlC01
C:8-270,C:461-500
1d
3inlD01
D:8-270,D:461-500
1e
3inlE01
E:8-270,E:461-500
1f
3inlF01
F:8-270,F:461-500
1g
3inlG01
G:8-270,G:461-500
1h
3inlH01
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
3inlA02
A:271-460
2b
3inlC02
C:271-460
2c
3inlD02
D:271-460
2d
3inlE02
E:271-460
2e
3inlF02
F:271-460
2f
3inlG02
G:271-460
2g
3inlH02
H:271-460
2h
3inlB02
B:271-460
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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