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2ONM
Biol. Unit 3
Info
Asym.Unit (976 KB)
Biol.Unit 1 (333 KB)
Biol.Unit 2 (336 KB)
Biol.Unit 3 (322 KB)
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(1)
Title
:
HUMAN MITOCHONDRIAL ALDEHYDE DEHYDROGENASE ASIAN VARIANT, ALDH2*2, COMPLEXED WITH NAD+
Authors
:
H. N. Larson, T. D. Hurley
Date
:
24 Jan 07 (Deposition) - 06 Mar 07 (Release) - 12 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Keywords
:
Oxidoreductase, Aldh, Nad, Rossmann Fold
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. N. Larson, J. Zhou, Z. Chen, J. S. Stamler, H. Weiner, T. D. Hurley
Structural And Functional Consequences Of Coenzyme Binding To The Inactive Asian Variant Of Mitochondrial Aldehyde Dehydrogenase: Roles Of Residues 475 And 487.
J. Biol. Chem. V. 282 12940 2007
[
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Hetero Components
(3, 11)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
1e: ADENOSINE-5'-DIPHOSPHATE (ADPe)
1f: ADENOSINE-5'-DIPHOSPHATE (ADPf)
1g: ADENOSINE-5'-DIPHOSPHATE (ADPg)
2a: 1,2-ETHANEDIOL (EDOa)
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)
3a: GUANIDINE (GAIa)
3b: GUANIDINE (GAIb)
3c: GUANIDINE (GAIc)
3d: GUANIDINE (GAId)
3e: GUANIDINE (GAIe)
3f: GUANIDINE (GAIf)
3g: GUANIDINE (GAIg)
3h: GUANIDINE (GAIh)
3i: GUANIDINE (GAIi)
5a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
5b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
5c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
5d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
5e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
5e: SODIUM ION (NAe)
5f: SODIUM ION (NAf)
5g: SODIUM ION (NAg)
5h: SODIUM ION (NAh)
5i: SODIUM ION (NAi)
5j: SODIUM ION (NAj)
5k: SODIUM ION (NAk)
5l: SODIUM ION (NAl)
5m: SODIUM ION (NAm)
5n: SODIUM ION (NAn)
5o: SODIUM ION (NAo)
5p: SODIUM ION (NAp)
5q: SODIUM ION (NAq)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
4
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
EDO
5
Ligand/Ion
1,2-ETHANEDIOL
3
GAI
2
Ligand/Ion
GUANIDINE
4
NA
-1
Ligand/Ion
SODIUM ION
5
NAD
-1
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(17, 17)
Info
All Sites
01: AC5 (SOFTWARE)
02: BC5 (SOFTWARE)
03: BC6 (SOFTWARE)
04: BC7 (SOFTWARE)
05: BC8 (SOFTWARE)
06: CC8 (SOFTWARE)
07: CC9 (SOFTWARE)
08: DC1 (SOFTWARE)
09: DC2 (SOFTWARE)
10: EC4 (SOFTWARE)
11: FC5 (SOFTWARE)
12: FC6 (SOFTWARE)
13: FC7 (SOFTWARE)
14: FC8 (SOFTWARE)
15: FC9 (SOFTWARE)
16: GC5 (SOFTWARE)
17: GC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
ASN K:275 , ALA K:290 , ALA K:293 , GLY K:305 , THR K:308
BINDING SITE FOR RESIDUE NA K 5012
02
BC5
SOFTWARE
THR I:39 , VAL I:40 , ASP I:109 , GLN I:196 , HOH I:2491
BINDING SITE FOR RESIDUE NA I 609
03
BC6
SOFTWARE
VAL J:40 , PRO J:42 , ASP J:109 , GLN J:196 , VAL J:345
BINDING SITE FOR RESIDUE NA J 610
04
BC7
SOFTWARE
VAL K:40 , ASP K:109 , GLN K:196
BINDING SITE FOR RESIDUE NA K 611
05
BC8
SOFTWARE
THR L:39 , VAL L:40 , ASP L:109 , GLN L:196
BINDING SITE FOR RESIDUE NA L 612
06
CC8
SOFTWARE
ILE I:165 , ILE I:166 , TRP I:168 , LYS I:192 , ALA I:194 , GLU I:195 , GLY I:225 , PRO I:226 , GLY I:229 , ALA I:230 , PHE I:243 , THR I:244 , GLY I:245 , SER I:246 , ILE I:249 , ILE I:253
BINDING SITE FOR RESIDUE ADP I 509
07
CC9
SOFTWARE
ILE J:165 , ILE J:166 , TRP J:168 , LYS J:192 , GLU J:195 , GLN J:196 , GLY J:225 , GLY J:229 , ALA J:230 , PHE J:243 , GLY J:245 , SER J:246 , ILE J:249 , ILE J:253
BINDING SITE FOR RESIDUE ADP J 510
08
DC1
SOFTWARE
ILE K:165 , ILE K:166 , TRP K:168 , LYS K:192 , GLU K:195 , GLY K:225 , GLY K:229 , ALA K:230 , PHE K:243 , GLY K:245 , SER K:246 , ILE K:249 , ILE K:253 , HOH K:1244
BINDING SITE FOR RESIDUE ADP K 511
09
DC2
SOFTWARE
ILE L:165 , ILE L:166 , TRP L:168 , LYS L:192 , GLU L:195 , GLY L:225 , GLY L:229 , ALA L:230 , PHE L:243 , SER L:246 , ILE L:249 , ILE L:253 , HOH L:2926
BINDING SITE FOR RESIDUE ADP L 512
10
EC4
SOFTWARE
PHE E:18 , TYR E:101 , TYR E:203 , HOH E:2787 , GLN I:14
BINDING SITE FOR RESIDUE EDO E 905
11
FC5
SOFTWARE
THR I:44 , GLU I:46
BINDING SITE FOR RESIDUE EDO I 809
12
FC6
SOFTWARE
PHE I:18 , TYR I:101 , TYR I:203 , HOH I:1775 , HOH I:2128
BINDING SITE FOR RESIDUE EDO I 909
13
FC7
SOFTWARE
TYR K:101 , TYR K:203 , HOH K:2794
BINDING SITE FOR RESIDUE EDO K 911
14
FC8
SOFTWARE
ASN K:440 , SER K:443 , TYR L:153 , ARG L:155
BINDING SITE FOR RESIDUE EDO L 712
15
FC9
SOFTWARE
PHE L:18 , TYR L:101 , TYR L:203
BINDING SITE FOR RESIDUE EDO L 912
16
GC5
SOFTWARE
ASP I:147 , GLY I:148 , PHE I:150
BINDING SITE FOR RESIDUE GAI I 910
17
GC6
SOFTWARE
PHE I:459 , ILE J:146 , ASP J:147
BINDING SITE FOR RESIDUE GAI J 611
[
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 I/J/K/L, )
2: VAR_011302 (E479K, chain I/J/K/L, )
3: VAR_002248 (K487K, chain I/J/K/L, )
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
I/J/K/L
E
320
V
2
UniProt
VAR_011302
E
496
K
ALDH2_HUMAN
Polymorphism
---
I/J/K/L
E
479
K
3
UniProt
VAR_002248
E
504
K
ALDH2_HUMAN
Polymorphism
671
I/J/K/L
K
487
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: ALDEHYDE_DEHYDR_GLU (I:267-274,J:267-274,K:267-274,L:26...)
2: ALDEHYDE_DEHYDR_CYS (I:295-306,J:295-306,K:295-306,L:29...)
;
View:
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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
-
-
-
-
-
-
-
-
I:267-274
J:267-274
K:267-274
L:267-274
2
ALDEHYDE_DEHYDR_CYS
PS00070
Aldehyde dehydrogenases cysteine active site.
ALDH2_HUMAN
312-323
4
-
-
-
-
-
-
-
-
I:295-306
J:295-306
K:295-306
L:295-306
[
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Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
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, 12)
Info
All SCOP Domains
1a: SCOP_d2onma_ (A:)
1b: SCOP_d2onmb_ (B:)
1c: SCOP_d2onmc_ (C:)
1d: SCOP_d2onmd_ (D:)
1e: SCOP_d2onme_ (E:)
1f: SCOP_d2onmf_ (F:)
1g: SCOP_d2onmg_ (G:)
1h: SCOP_d2onmh_ (H:)
1i: SCOP_d2onmi_ (I:)
1j: SCOP_d2onmj_ (J:)
1k: SCOP_d2onmk_ (K:)
1l: SCOP_d2onml_ (L:)
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)
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)
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)
(
)
Families
(
)
(
)
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
d2onma_
A:
1b
d2onmb_
B:
1c
d2onmc_
C:
1d
d2onmd_
D:
1e
d2onme_
E:
1f
d2onmf_
F:
1g
d2onmg_
G:
1h
d2onmh_
H:
1i
d2onmi_
I:
1j
d2onmj_
J:
1k
d2onmk_
K:
1l
d2onml_
L:
[
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]
CATH Domains
(2, 24)
Info
all CATH domains
1a: CATH_2onmA01 (A:8-270,A:461-500)
1b: CATH_2onmE01 (E:8-270,E:461-500)
1c: CATH_2onmF01 (F:8-270,F:461-500)
1d: CATH_2onmG01 (G:8-270,G:461-500)
1e: CATH_2onmH01 (H:8-270,H:461-500)
1f: CATH_2onmI01 (I:8-270,I:461-500)
1g: CATH_2onmJ01 (J:8-270,J:461-500)
1h: CATH_2onmK01 (K:8-270,K:461-500)
1i: CATH_2onmL01 (L:8-270,L:461-500)
1j: CATH_2onmB01 (B:8-270,B:461-500)
1k: CATH_2onmC01 (C:8-270,C:461-500)
1l: CATH_2onmD01 (D:8-270,D:461-500)
2a: CATH_2onmA02 (A:271-460)
2b: CATH_2onmB02 (B:271-460)
2c: CATH_2onmC02 (C:271-460)
2d: CATH_2onmD02 (D:271-460)
2e: CATH_2onmE02 (E:271-460)
2f: CATH_2onmF02 (F:271-460)
2g: CATH_2onmG02 (G:271-460)
2h: CATH_2onmH02 (H:271-460)
2i: CATH_2onmI02 (I:271-460)
2j: CATH_2onmJ02 (J:271-460)
2k: CATH_2onmK02 (K:271-460)
2l: CATH_2onmL02 (L:271-460)
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Classes
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)
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Architectures
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)
(
)
Topologies
(
)
(
)
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
2onmA01
A:8-270,A:461-500
1b
2onmE01
E:8-270,E:461-500
1c
2onmF01
F:8-270,F:461-500
1d
2onmG01
G:8-270,G:461-500
1e
2onmH01
H:8-270,H:461-500
1f
2onmI01
I:8-270,I:461-500
1g
2onmJ01
J:8-270,J:461-500
1h
2onmK01
K:8-270,K:461-500
1i
2onmL01
L:8-270,L:461-500
1j
2onmB01
B:8-270,B:461-500
1k
2onmC01
C:8-270,C:461-500
1l
2onmD01
D:8-270,D:461-500
Topology
:
Aldehyde Dehydrogenase; Chain A, domain 2
(89)
Homologous Superfamily
:
Aldehyde Dehydrogenase; Chain A, domain 2
(89)
Human (Homo sapiens)
(22)
2a
2onmA02
A:271-460
2b
2onmB02
B:271-460
2c
2onmC02
C:271-460
2d
2onmD02
D:271-460
2e
2onmE02
E:271-460
2f
2onmF02
F:271-460
2g
2onmG02
G:271-460
2h
2onmH02
H:271-460
2i
2onmI02
I:271-460
2j
2onmJ02
J:271-460
2k
2onmK02
K:271-460
2l
2onmL02
L:271-460
[
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]
Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_Aldedh_2onmL01 (L:28-491)
1b: PFAM_Aldedh_2onmL02 (L:28-491)
1c: PFAM_Aldedh_2onmL03 (L:28-491)
1d: PFAM_Aldedh_2onmL04 (L:28-491)
1e: PFAM_Aldedh_2onmL05 (L:28-491)
1f: PFAM_Aldedh_2onmL06 (L:28-491)
1g: PFAM_Aldedh_2onmL07 (L:28-491)
1h: PFAM_Aldedh_2onmL08 (L:28-491)
1i: PFAM_Aldedh_2onmL09 (L:28-491)
1j: PFAM_Aldedh_2onmL10 (L:28-491)
1k: PFAM_Aldedh_2onmL11 (L:28-491)
1l: PFAM_Aldedh_2onmL12 (L:28-491)
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Clans
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Families
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)
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)
Organisms
(
)
(
)
Clan
:
ALDH-like
(49)
Family
:
Aldedh
(45)
Homo sapiens (Human)
(21)
1a
Aldedh-2onmL01
L:28-491
1b
Aldedh-2onmL02
L:28-491
1c
Aldedh-2onmL03
L:28-491
1d
Aldedh-2onmL04
L:28-491
1e
Aldedh-2onmL05
L:28-491
1f
Aldedh-2onmL06
L:28-491
1g
Aldedh-2onmL07
L:28-491
1h
Aldedh-2onmL08
L:28-491
1i
Aldedh-2onmL09
L:28-491
1j
Aldedh-2onmL10
L:28-491
1k
Aldedh-2onmL11
L:28-491
1l
Aldedh-2onmL12
L:28-491
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Asym.Unit (976 KB)
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