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1O01
Biol. Unit 1
Info
Asym.Unit (701 KB)
Biol.Unit 1 (352 KB)
Biol.Unit 2 (348 KB)
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(1)
Title
:
HUMAN MITOCHONDRIAL ALDEHYDE DEHYDROGENASE COMPLEXED WITH CROTONALDEHYDE, NAD(H) AND 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
:
2.15
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
(4, 15)
Info
All Hetero Components
1a: (2E)-BUT-2-ENAL (CRDa)
1b: (2E)-BUT-2-ENAL (CRDb)
1c: (2E)-BUT-2-ENAL (CRDc)
1d: (2E)-BUT-2-ENAL (CRDd)
1e: (2E)-BUT-2-ENAL (CRDe)
1f: (2E)-BUT-2-ENAL (CRDf)
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)
3a: GUANIDINE (GAIa)
3b: GUANIDINE (GAIb)
3c: GUANIDINE (GAIc)
3d: GUANIDINE (GAId)
3e: GUANIDINE (GAIe)
3f: GUANIDINE (GAIf)
3g: GUANIDINE (GAIg)
3h: GUANIDINE (GAIh)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
4g: MAGNESIUM ION (MGg)
4h: MAGNESIUM ION (MGh)
6a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
6b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
6c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
6d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
6e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
6f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
6g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
6h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
5d: SODIUM ION (NAd)
6e: SODIUM ION (NAe)
6f: SODIUM ION (NAf)
6g: SODIUM ION (NAg)
6h: SODIUM ION (NAh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CRD
3
Ligand/Ion
(2E)-BUT-2-ENAL
2
EDO
4
Ligand/Ion
1,2-ETHANEDIOL
3
GAI
4
Ligand/Ion
GUANIDINE
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
NA
-1
Ligand/Ion
SODIUM ION
6
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
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Sites
(23, 23)
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: CC5 (SOFTWARE)
13: CC6 (SOFTWARE)
14: CC7 (SOFTWARE)
15: CC8 (SOFTWARE)
16: DC4 (SOFTWARE)
17: DC5 (SOFTWARE)
18: DC6 (SOFTWARE)
19: DC7 (SOFTWARE)
20: EC3 (SOFTWARE)
21: EC4 (SOFTWARE)
22: EC5 (SOFTWARE)
23: EC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
NAD A:5501 , HOH A:5513 , HOH A:5524 , HOH A:5830
BINDING SITE FOR RESIDUE MG A 4601
02
AC2
SOFTWARE
NAD B:5502 , HOH B:5543
BINDING SITE FOR RESIDUE MG B 4602
03
AC3
SOFTWARE
NAD C:5503 , HOH C:5927
BINDING SITE FOR RESIDUE MG C 4603
04
AC4
SOFTWARE
NAD D:5504 , HOH D:5676 , HOH D:5679
BINDING SITE FOR RESIDUE MG D 4604
05
AC9
SOFTWARE
THR A:39 , VAL A:40 , ASP A:109 , GLN A:196 , HOH A:5531
BINDING SITE FOR RESIDUE NA A 4701
06
BC1
SOFTWARE
THR B:39 , VAL B:40 , ASP B:109 , GLN B:196 , HOH B:5982
BINDING SITE FOR RESIDUE NA B 4702
07
BC2
SOFTWARE
THR C:39 , VAL C:40 , ASP C:109 , GLN C:196 , HOH C:5665 , HOH C:5666
BINDING SITE FOR RESIDUE NA C 4703
08
BC3
SOFTWARE
THR D:39 , VAL D:40 , ASP D:109 , GLN D:196 , HOH D:5704
BINDING SITE FOR RESIDUE NA D 4704
09
BC8
SOFTWARE
PHE B:170 , CYS B:301 , CYS B:302 , PHE B:459
BINDING SITE FOR RESIDUE CRD B 4512
10
BC9
SOFTWARE
PHE C:170 , CYS C:301 , CYS C:302 , NAD C:5503
BINDING SITE FOR RESIDUE CRD C 4513
11
CC1
SOFTWARE
ASN D:169 , PHE D:170 , CYS D:301 , CYS D:302 , PHE D:459 , NAD D:5504
BINDING SITE FOR RESIDUE CRD D 4514
12
CC5
SOFTWARE
PHE A:70 , GLU A:157 , PRO A:158 , VAL A:159 , HOH A:5711 , HOH A:5712 , HOH A:5714 , TYR B:468
BINDING SITE FOR RESIDUE GAI A 4801
13
CC6
SOFTWARE
TYR A:468 , GLU B:157 , PRO B:158 , VAL B:159 , HOH B:5697
BINDING SITE FOR RESIDUE GAI B 4802
14
CC7
SOFTWARE
GLU C:157 , PRO C:158 , VAL C:159 , HOH C:5793 , TYR D:468
BINDING SITE FOR RESIDUE GAI C 4803
15
CC8
SOFTWARE
TYR C:468 , GLU D:157 , PRO D:158 , VAL D:159 , HOH D:5775 , HOH D:5777
BINDING SITE FOR RESIDUE GAI D 4804
16
DC4
SOFTWARE
TYR A:153 , ARG A:155 , SER B:443 , PHE D:151 , HOH D:5760
BINDING SITE FOR RESIDUE EDO D 4901
17
DC5
SOFTWARE
ASN A:440 , SER A:443 , TYR B:153 , ARG B:155 , PHE C:151
BINDING SITE FOR RESIDUE EDO C 4902
18
DC6
SOFTWARE
PHE B:151 , TYR C:153 , ARG C:155 , SER D:443
BINDING SITE FOR RESIDUE EDO C 4903
19
DC7
SOFTWARE
PHE A:151 , SER C:443 , TYR D:153 , ARG D:155 , HOH D:5770
BINDING SITE FOR RESIDUE EDO D 4904
20
EC3
SOFTWARE
ILE A:165 , ILE A:166 , PRO A:167 , TRP A:168 , ASN A:169 , LYS A:192 , ALA A:194 , 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 , LEU A:269 , CYS A:302 , GLN A:349 , GLU A:399 , PHE A:401 , MG A:4601 , HOH A:5512 , HOH A:5525 , HOH A:5794 , HOH A:5801 , HOH A:5934 , HOH A:5936
BINDING SITE FOR RESIDUE NAD A 5501
21
EC4
SOFTWARE
ILE B:165 , ILE B:166 , PRO B:167 , TRP B:168 , ASN B:169 , LYS B:192 , GLU B:195 , GLN B:196 , GLY B:225 , GLY B:229 , ALA B:230 , PHE B:243 , GLY B:245 , SER B:246 , ILE B:249 , ILE B:253 , LEU B:269 , GLY B:270 , CYS B:302 , GLN B:349 , GLU B:399 , PHE B:401 , MG B:4602 , HOH B:5532 , HOH B:5533 , HOH B:5543 , HOH B:5544 , HOH B:5694 , HOH B:5972 , HOH B:5976
BINDING SITE FOR RESIDUE NAD B 5502
22
EC5
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 , LEU C:269 , GLY C:270 , CYS C:302 , GLN C:349 , LYS C:352 , GLU C:399 , PHE C:401 , CRD C:4513 , MG C:4603 , HOH C:5614 , HOH C:5615 , HOH C:5618 , HOH C:5620 , HOH C:5868 , HOH C:5925 , HOH C:5926
BINDING SITE FOR RESIDUE NAD C 5503
23
EC6
SOFTWARE
ILE D:165 , ILE D:166 , PRO D:167 , TRP D:168 , ASN D:169 , LYS D:192 , GLU D:195 , GLN D:196 , GLY D:225 , GLY D:229 , ALA D:230 , PHE D:243 , GLY D:245 , SER D:246 , ILE D:249 , ILE D:253 , LEU D:269 , GLY D:270 , CYS D:302 , GLN D:349 , LYS D:352 , GLU D:399 , PHE D:401 , CRD D:4514 , MG D:4604 , HOH D:5681 , HOH D:5684 , HOH D:5685 , HOH D:5710 , HOH D:5910
BINDING SITE FOR RESIDUE NAD D 5504
[
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]
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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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
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
View:
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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_d1o01a_ (A:)
1b: SCOP_d1o01b_ (B:)
1c: SCOP_d1o01c_ (C:)
1d: SCOP_d1o01d_ (D:)
1e: SCOP_d1o01e_ (E:)
1f: SCOP_d1o01f_ (F:)
1g: SCOP_d1o01g_ (G:)
1h: SCOP_d1o01h_ (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
d1o01a_
A:
1b
d1o01b_
B:
1c
d1o01c_
C:
1d
d1o01d_
D:
1e
d1o01e_
E:
1f
d1o01f_
F:
1g
d1o01g_
G:
1h
d1o01h_
H:
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_1o01A01 (A:8-270,A:461-500)
1b: CATH_1o01B01 (B:8-270,B:461-500)
1c: CATH_1o01C01 (C:8-270,C:461-500)
1d: CATH_1o01D01 (D:8-270,D:461-500)
1e: CATH_1o01E01 (E:8-270,E:461-500)
1f: CATH_1o01F01 (F:8-270,F:461-500)
1g: CATH_1o01G01 (G:8-270,G:461-500)
1h: CATH_1o01H01 (H:8-270,H:461-500)
2a: CATH_1o01A02 (A:271-460)
2b: CATH_1o01B02 (B:271-460)
2c: CATH_1o01C02 (C:271-460)
2d: CATH_1o01D02 (D:271-460)
2e: CATH_1o01E02 (E:271-460)
2f: CATH_1o01F02 (F:271-460)
2g: CATH_1o01G02 (G:271-460)
2h: CATH_1o01H02 (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
1o01A01
A:8-270,A:461-500
1b
1o01B01
B:8-270,B:461-500
1c
1o01C01
C:8-270,C:461-500
1d
1o01D01
D:8-270,D:461-500
1e
1o01E01
E:8-270,E:461-500
1f
1o01F01
F:8-270,F:461-500
1g
1o01G01
G:8-270,G:461-500
1h
1o01H01
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
1o01A02
A:271-460
2b
1o01B02
B:271-460
2c
1o01C02
C:271-460
2d
1o01D02
D:271-460
2e
1o01E02
E:271-460
2f
1o01F02
F:271-460
2g
1o01G02
G:271-460
2h
1o01H02
H:271-460
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (701 KB)
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