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1O02
Biol. Unit 1
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: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC3 (SOFTWARE)
09: BC8 (SOFTWARE)
10: BC9 (SOFTWARE)
11: CC1 (SOFTWARE)
12: CC2 (SOFTWARE)
13: CC7 (SOFTWARE)
14: CC8 (SOFTWARE)
15: CC9 (SOFTWARE)
16: DC1 (SOFTWARE)
17: DC6 (SOFTWARE)
18: DC7 (SOFTWARE)
19: DC8 (SOFTWARE)
20: DC9 (SOFTWARE)
21: EC5 (SOFTWARE)
22: EC6 (SOFTWARE)
23: EC7 (SOFTWARE)
24: EC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
NAD A:5501 , HOH A:5532 , HOH A:5534 , HOH A:5667 , HOH A:5668
BINDING SITE FOR RESIDUE MG A 4601
02
AC2
SOFTWARE
NAD B:5502 , HOH B:5587 , HOH B:5588 , HOH B:5589 , HOH B:5590
BINDING SITE FOR RESIDUE MG B 4602
03
AC3
SOFTWARE
NAD C:5503 , HOH C:5840 , HOH C:5841 , HOH C:5867 , HOH C:5868
BINDING SITE FOR RESIDUE MG C 4603
04
AC4
SOFTWARE
NAD D:5504 , HOH D:5521 , HOH D:5522 , HOH D:5523 , HOH D:5524
BINDING SITE FOR RESIDUE MG D 4604
05
AC9
SOFTWARE
THR A:39 , VAL A:40 , ASP A:109 , GLN A:196 , HOH A:5720
BINDING SITE FOR RESIDUE NA A 4701
06
BC1
SOFTWARE
THR B:39 , VAL B:40 , ASP B:109 , GLN B:196 , HOH B:5599
BINDING SITE FOR RESIDUE NA B 4702
07
BC2
SOFTWARE
THR C:39 , VAL C:40 , ASP C:109 , GLN C:196 , HOH C:5857
BINDING SITE FOR RESIDUE NA C 4703
08
BC3
SOFTWARE
THR D:39 , VAL D:40 , ASP D:109 , GLN D:196 , HOH D:5924 , HOH D:5925
BINDING SITE FOR RESIDUE NA D 4704
09
BC8
SOFTWARE
PHE A:70 , GLU A:157 , PRO A:158 , VAL A:159 , HOH A:5903 , HOH A:5904 , TYR B:468
BINDING SITE FOR RESIDUE GAI A 4801
10
BC9
SOFTWARE
TYR A:468 , GLU B:157 , PRO B:158 , VAL B:159 , HOH B:5553 , HOH B:5798 , HOH B:5800
BINDING SITE FOR RESIDUE GAI B 4802
11
CC1
SOFTWARE
GLU C:157 , PRO C:158 , VAL C:159 , HOH C:5524 , TYR D:468
BINDING SITE FOR RESIDUE GAI C 4803
12
CC2
SOFTWARE
TYR C:468 , GLU D:157 , PRO D:158 , VAL D:159
BINDING SITE FOR RESIDUE GAI D 4804
13
CC7
SOFTWARE
ILE A:146 , ASP A:147 , PHE A:150 , HOH A:5554 , HOH A:5559 , PHE B:459
BINDING SITE FOR RESIDUE GAI A 4811
14
CC8
SOFTWARE
PHE A:459 , HOH A:5699 , ILE B:146 , ASP B:147 , PHE B:150 , HOH B:5845
BINDING SITE FOR RESIDUE GAI B 4812
15
CC9
SOFTWARE
ASP C:147 , PHE C:150 , HOH C:5666 , HOH C:5671 , PHE D:459 , HOH D:5812
BINDING SITE FOR RESIDUE GAI C 4813
16
DC1
SOFTWARE
PHE C:459 , HOH C:5556 , ILE D:146 , ASP D:147 , PHE D:150
BINDING SITE FOR RESIDUE GAI D 4814
17
DC6
SOFTWARE
TYR A:153 , ARG A:155 , HOH A:5875 , SER B:443 , PHE D:151
BINDING SITE FOR RESIDUE EDO A 4901
18
DC7
SOFTWARE
SER A:443 , TYR B:153 , ARG B:155 , PHE C:151
BINDING SITE FOR RESIDUE EDO B 4902
19
DC8
SOFTWARE
PHE B:151 , TYR C:153 , ARG C:155 , SER D:443
BINDING SITE FOR RESIDUE EDO C 4903
20
DC9
SOFTWARE
PHE A:151 , SER C:443 , TYR D:153 , ARG D:155
BINDING SITE FOR RESIDUE EDO D 4904
21
EC5
SOFTWARE
ILE A:165 , ILE A:166 , PRO A:167 , TRP A:168 , ASN A:169 , LYS A:192 , GLU A:195 , GLY A:225 , GLY A:229 , ALA A:230 , PHE A:243 , GLY A:245 , SER A:246 , ILE A:249 , ILE A:253 , GLU A:268 , LEU A:269 , CYS A:302 , GLN A:349 , GLU A:399 , PHE A:401 , MG A:4601 , HOH A:5529 , HOH A:5530 , HOH A:5532 , HOH A:5535 , HOH A:5536 , HOH A:5539 , HOH A:5652 , HOH A:5667 , HOH A:5668 , HOH A:5917
BINDING SITE FOR RESIDUE NAD A 5501
22
EC6
SOFTWARE
ILE B:165 , ILE B:166 , PRO B:167 , TRP B:168 , ASN B:169 , LYS B:192 , GLU B:195 , GLY B:225 , PRO B:226 , GLY B:229 , ALA B:230 , PHE B:243 , GLY B:245 , SER B:246 , ILE B:249 , ILE B:253 , GLU B:268 , LEU B:269 , CYS B:302 , GLN B:349 , GLU B:399 , PHE B:401 , MG B:4602 , HOH B:5515 , HOH B:5577 , HOH B:5578 , HOH B:5587 , HOH B:5588 , HOH B:5590 , HOH B:5592 , HOH B:5901 , HOH B:5902 , HOH B:5998
BINDING SITE FOR RESIDUE NAD B 5502
23
EC7
SOFTWARE
ILE C:165 , ILE C:166 , PRO C:167 , TRP C:168 , ASN C:169 , LYS C:192 , ALA C:194 , GLU C:195 , GLN C:196 , GLY C:225 , GLY C:229 , ALA C:230 , PHE C:243 , GLY C:245 , SER C:246 , ILE C:249 , ILE C:253 , GLU C:268 , LEU C:269 , CYS C:302 , GLN C:349 , LYS C:352 , GLU C:399 , PHE C:401 , MG C:4603 , HOH C:5770 , HOH C:5772 , HOH C:5839 , HOH C:5840 , HOH C:5852 , HOH C:5853 , HOH C:5867 , HOH C:5868 , HOH C:5869
BINDING SITE FOR RESIDUE NAD C 5503
24
EC8
SOFTWARE
ILE D:165 , ILE D:166 , PRO D:167 , TRP D:168 , ASN D:169 , LYS D:192 , GLU D:195 , GLY D:225 , GLY D:229 , ALA D:230 , PHE D:243 , GLY D:245 , SER D:246 , ILE D:249 , ILE D:253 , GLU D:268 , LEU D:269 , CYS D:302 , GLN D:349 , LYS D:352 , GLU D:399 , PHE D:401 , MG D:4604 , HOH D:5519 , HOH D:5521 , HOH D:5522 , HOH D:5525 , HOH D:5526 , HOH D:5533 , HOH D:5830 , HOH D:5885
BINDING SITE FOR RESIDUE NAD D 5504
[
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 A/B/C/D, )
2: VAR_011302 (E479K, chain A/B/C/D, )
3: VAR_002248 (E487K, chain A/B/C/D, )
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
320
V
2
UniProt
VAR_011302
E
496
K
ALDH2_HUMAN
Polymorphism
---
A/B/C/D
E
479
K
3
UniProt
VAR_002248
E
504
K
ALDH2_HUMAN
Polymorphism
671
A/B/C/D
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 (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:
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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
A:267-274
B:267-274
C:267-274
D:267-274
-
-
-
-
2
ALDEHYDE_DEHYDR_CYS
PS00070
Aldehyde dehydrogenases cysteine active site.
ALDH2_HUMAN
312-323
4
A:295-306
B:295-306
C:295-306
D:295-306
-
-
-
-
[
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]
Exons
(0, 0)
Info
All Exons
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Label:
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
(
)
(
)
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
(
)
(
)
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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