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1O02
Biol. Unit 2
Info
Asym.Unit (698 KB)
Biol.Unit 1 (349 KB)
Biol.Unit 2 (348 KB)
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(1)
Title
:
HUMAN MITOCHONDRIAL ALDEHYDE DEHYDROGENASE COMPLEXED WITH NADH IN THE PRESENCE OF MG2+
Authors
:
S. J. Perez-Miller, T. D. Hurley
Date
:
20 Feb 03 (Deposition) - 24 Jun 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
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
:
Aldh, Nad, Nadh, Isomerization, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. J. Perez-Miller, T. D. Hurley
Coenzyme Isomerization Is Integral To Catalysis In Aldehyde Dehydrogenase
Biochemistry V. 42 7100 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 16)
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)
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)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
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)
5f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
5g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
5h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
4
Ligand/Ion
1,2-ETHANEDIOL
2
GAI
8
Ligand/Ion
GUANIDINE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
NA
-1
Ligand/Ion
SODIUM ION
5
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(24, 24)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: BC4 (SOFTWARE)
06: BC5 (SOFTWARE)
07: BC6 (SOFTWARE)
08: BC7 (SOFTWARE)
09: CC3 (SOFTWARE)
10: CC4 (SOFTWARE)
11: CC5 (SOFTWARE)
12: CC6 (SOFTWARE)
13: DC2 (SOFTWARE)
14: DC3 (SOFTWARE)
15: DC4 (SOFTWARE)
16: DC5 (SOFTWARE)
17: EC1 (SOFTWARE)
18: EC2 (SOFTWARE)
19: EC3 (SOFTWARE)
20: EC4 (SOFTWARE)
21: EC9 (SOFTWARE)
22: FC1 (SOFTWARE)
23: FC2 (SOFTWARE)
24: FC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
HOH E:2271 , HOH E:2272 , HOH E:2761 , HOH E:2762 , NAD E:5505
BINDING SITE FOR RESIDUE MG E 4605
02
AC6
SOFTWARE
HOH F:2164 , HOH F:2165 , HOH F:2197 , HOH F:2198 , NAD F:5506
BINDING SITE FOR RESIDUE MG F 4606
03
AC7
SOFTWARE
HOH G:1900 , HOH G:1901 , HOH G:1902 , HOH G:1903 , NAD G:5507
BINDING SITE FOR RESIDUE MG G 4607
04
AC8
SOFTWARE
HOH H:1860 , HOH H:1865 , HOH H:1866 , HOH H:1867 , NAD H:5508
BINDING SITE FOR RESIDUE MG H 4608
05
BC4
SOFTWARE
THR E:39 , VAL E:40 , ASP E:109 , GLN E:196 , HOH E:3137
BINDING SITE FOR RESIDUE NA E 4705
06
BC5
SOFTWARE
THR F:39 , VAL F:40 , ASP F:109 , GLN F:196 , HOH F:2712
BINDING SITE FOR RESIDUE NA F 4706
07
BC6
SOFTWARE
THR G:39 , VAL G:40 , ASP G:109 , GLN G:196 , HOH G:1912
BINDING SITE FOR RESIDUE NA G 4707
08
BC7
SOFTWARE
THR H:39 , VAL H:40 , ASP H:109 , GLN H:196 , HOH H:1850
BINDING SITE FOR RESIDUE NA H 4708
09
CC3
SOFTWARE
GLU E:157 , PRO E:158 , VAL E:159 , TYR F:468
BINDING SITE FOR RESIDUE GAI E 4805
10
CC4
SOFTWARE
TYR E:468 , GLU F:157 , PRO F:158 , VAL F:159 , HOH F:2116 , HOH F:2117
BINDING SITE FOR RESIDUE GAI F 4806
11
CC5
SOFTWARE
GLU G:157 , PRO G:158 , VAL G:159 , HOH G:3480 , HOH G:3481 , TYR H:468
BINDING SITE FOR RESIDUE GAI G 4807
12
CC6
SOFTWARE
TYR G:468 , GLU H:157 , PRO H:158 , VAL H:159 , HOH H:2442 , HOH H:2443
BINDING SITE FOR RESIDUE GAI H 4808
13
DC2
SOFTWARE
ASP E:147 , PHE E:150 , PHE F:459 , HOH F:3281
BINDING SITE FOR RESIDUE GAI E 4815
14
DC3
SOFTWARE
PHE E:459 , HOH E:3101 , ILE F:146 , ASP F:147 , PHE F:150
BINDING SITE FOR RESIDUE GAI F 4816
15
DC4
SOFTWARE
ILE G:146 , ASP G:147 , PHE G:150 , HOH G:3334 , PHE H:459 , HOH H:3079
BINDING SITE FOR RESIDUE GAI G 4817
16
DC5
SOFTWARE
PHE G:459 , HOH G:3020 , ILE H:146 , ASP H:147 , PHE H:150
BINDING SITE FOR RESIDUE GAI G 4818
17
EC1
SOFTWARE
TYR E:153 , ARG E:155 , HOH E:2863 , SER F:443 , PHE H:151
BINDING SITE FOR RESIDUE EDO E 4905
18
EC2
SOFTWARE
SER E:443 , TYR F:153 , ARG F:155 , PHE G:151
BINDING SITE FOR RESIDUE EDO F 4906
19
EC3
SOFTWARE
PHE F:151 , HOH F:2524 , TYR G:153 , ARG G:155 , SER H:443
BINDING SITE FOR RESIDUE EDO F 4907
20
EC4
SOFTWARE
PHE E:151 , SER G:443 , TYR H:153 , ARG H:155
BINDING SITE FOR RESIDUE EDO H 4908
21
EC9
SOFTWARE
ILE E:165 , ILE E:166 , PRO E:167 , TRP E:168 , ASN E:169 , LYS E:192 , GLU E:195 , GLN E:196 , GLY E:225 , GLY E:229 , ALA E:230 , PHE E:243 , GLY E:245 , SER E:246 , ILE E:249 , ILE E:253 , GLU E:268 , LEU E:269 , CYS E:302 , GLN E:349 , GLU E:399 , PHE E:401 , HOH E:2266 , HOH E:2267 , HOH E:2271 , HOH E:2273 , HOH E:2274 , HOH E:2276 , HOH E:2761 , HOH E:2762 , HOH E:2764 , HOH E:3160 , MG E:4605
BINDING SITE FOR RESIDUE NAD E 5505
22
FC1
SOFTWARE
ILE F:165 , ILE F:166 , PRO F:167 , TRP F:168 , ASN F:169 , LYS F:192 , GLU F:195 , GLN F:196 , GLY F:225 , PRO F:226 , GLY F:229 , ALA F:230 , PHE F:243 , GLY F:245 , SER F:246 , ILE F:249 , ILE F:253 , GLU F:268 , LEU F:269 , CYS F:302 , GLN F:349 , LYS F:352 , GLU F:399 , PHE F:401 , HOH F:2158 , HOH F:2162 , HOH F:2163 , HOH F:2165 , HOH F:2167 , HOH F:2185 , HOH F:2186 , HOH F:2197 , HOH F:2198 , HOH F:2675 , MG F:4606
BINDING SITE FOR RESIDUE NAD F 5506
23
FC2
SOFTWARE
ILE G:165 , ILE G:166 , PRO G:167 , TRP G:168 , ASN G:169 , LYS G:192 , ALA G:194 , GLU G:195 , GLY G:225 , GLY G:229 , ALA G:230 , PHE G:243 , GLY G:245 , SER G:246 , ILE G:249 , ILE G:253 , GLU G:268 , LEU G:269 , CYS G:302 , GLN G:349 , LYS G:352 , GLU G:399 , PHE G:401 , HOH G:1898 , HOH G:1899 , HOH G:1901 , HOH G:1902 , HOH G:1903 , HOH G:1904 , HOH G:1905 , HOH G:1930 , HOH G:1931 , HOH G:2464 , HOH G:3473 , MG G:4607
BINDING SITE FOR RESIDUE NAD G 5507
24
FC3
SOFTWARE
ILE H:165 , ILE H:166 , PRO H:167 , TRP H:168 , ASN H:169 , LYS H:192 , ALA H:194 , GLU H:195 , GLN H:196 , GLY H:225 , GLY H:229 , ALA H:230 , PHE H:243 , GLY H:245 , SER H:246 , ILE H:249 , ILE H:253 , GLU H:268 , LEU H:269 , CYS H:302 , GLN H:349 , GLU H:399 , PHE H:401 , HOH H:1137 , HOH H:1138 , HOH H:1859 , HOH H:1860 , HOH H:1862 , HOH H:1864 , HOH H:1868 , HOH H:1870 , HOH H:1890 , MG H:4608
BINDING SITE FOR RESIDUE NAD H 5508
[
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 (E487K, 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
E
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 (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:
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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
-
-
-
-
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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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_d1o02a_ (A:)
1b: SCOP_d1o02b_ (B:)
1c: SCOP_d1o02c_ (C:)
1d: SCOP_d1o02d_ (D:)
1e: SCOP_d1o02e_ (E:)
1f: SCOP_d1o02f_ (F:)
1g: SCOP_d1o02g_ (G:)
1h: SCOP_d1o02h_ (H:)
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)
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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
d1o02a_
A:
1b
d1o02b_
B:
1c
d1o02c_
C:
1d
d1o02d_
D:
1e
d1o02e_
E:
1f
d1o02f_
F:
1g
d1o02g_
G:
1h
d1o02h_
H:
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_1o02A01 (A:8-270,A:461-500)
1b: CATH_1o02B01 (B:8-270,B:461-500)
1c: CATH_1o02C01 (C:8-270,C:461-500)
1d: CATH_1o02D01 (D:8-270,D:461-500)
1e: CATH_1o02E01 (E:8-270,E:461-500)
1f: CATH_1o02F01 (F:8-270,F:461-500)
1g: CATH_1o02G01 (G:8-270,G:461-500)
1h: CATH_1o02H01 (H:8-270,H:461-500)
2a: CATH_1o02A02 (A:271-460)
2b: CATH_1o02B02 (B:271-460)
2c: CATH_1o02C02 (C:271-460)
2d: CATH_1o02D02 (D:271-460)
2e: CATH_1o02E02 (E:271-460)
2f: CATH_1o02F02 (F:271-460)
2g: CATH_1o02G02 (G:271-460)
2h: CATH_1o02H02 (H: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
1o02A01
A:8-270,A:461-500
1b
1o02B01
B:8-270,B:461-500
1c
1o02C01
C:8-270,C:461-500
1d
1o02D01
D:8-270,D:461-500
1e
1o02E01
E:8-270,E:461-500
1f
1o02F01
F:8-270,F:461-500
1g
1o02G01
G:8-270,G:461-500
1h
1o02H01
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
1o02A02
A:271-460
2b
1o02B02
B:271-460
2c
1o02C02
C:271-460
2d
1o02D02
D:271-460
2e
1o02E02
E:271-460
2f
1o02F02
F:271-460
2g
1o02G02
G:271-460
2h
1o02H02
H:271-460
[
close CATH info
]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Aldedh_1o02H01 (H:28-491)
1b: PFAM_Aldedh_1o02H02 (H:28-491)
1c: PFAM_Aldedh_1o02H03 (H:28-491)
1d: PFAM_Aldedh_1o02H04 (H:28-491)
1e: PFAM_Aldedh_1o02H05 (H:28-491)
1f: PFAM_Aldedh_1o02H06 (H:28-491)
1g: PFAM_Aldedh_1o02H07 (H:28-491)
1h: PFAM_Aldedh_1o02H08 (H:28-491)
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Clans
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Organisms
(
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(
)
Clan
:
ALDH-like
(49)
Family
:
Aldedh
(45)
Homo sapiens (Human)
(21)
1a
Aldedh-1o02H01
H:28-491
1b
Aldedh-1o02H02
H:28-491
1c
Aldedh-1o02H03
H:28-491
1d
Aldedh-1o02H04
H:28-491
1e
Aldedh-1o02H05
H:28-491
1f
Aldedh-1o02H06
H:28-491
1g
Aldedh-1o02H07
H:28-491
1h
Aldedh-1o02H08
H:28-491
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Asym.Unit (698 KB)
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