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1O00
Asym. Unit
Info
Asym.Unit (668 KB)
Biol.Unit 1 (333 KB)
Biol.Unit 2 (333 KB)
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(1)
Title
:
HUMAN MITOCHONDRIAL ALDEHYDE DEHYDROGENASE COMPLEXED WITH NAD+ AND MG2+ SHOWING DUAL NAD(H) CONFORMATIONS
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
:
2.60
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
)
[
close entry info
]
Hetero Components
(3, 24)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
1g: MAGNESIUM ION (MGg)
1h: MAGNESIUM ION (MGh)
3a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
3b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
3d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
3e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
3f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
3g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
3h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
2c: SODIUM ION (NAc)
2d: 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
MG
8
Ligand/Ion
MAGNESIUM ION
2
NA
8
Ligand/Ion
SODIUM ION
3
NAD
8
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: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
NAD A:1502
BINDING SITE FOR RESIDUE MG A 2601
02
AC2
SOFTWARE
NAD B:2502
BINDING SITE FOR RESIDUE MG B 2602
03
AC3
SOFTWARE
NAD C:3502
BINDING SITE FOR RESIDUE MG C 2603
04
AC4
SOFTWARE
NAD D:4502
BINDING SITE FOR RESIDUE MG D 2604
05
AC5
SOFTWARE
VAL A:40 , ASP A:109 , GLN A:196
BINDING SITE FOR RESIDUE NA A 2701
06
AC6
SOFTWARE
THR B:39 , VAL B:40 , ASP B:109 , GLN B:196
BINDING SITE FOR RESIDUE NA B 2702
07
AC7
SOFTWARE
VAL C:40 , ASP C:109 , GLN C:196
BINDING SITE FOR RESIDUE NA C 2703
08
AC8
SOFTWARE
THR D:39 , VAL D:40 , ASP D:109 , GLN D:196
BINDING SITE FOR RESIDUE NA D 2704
09
AC9
SOFTWARE
NAD E:5502
BINDING SITE FOR RESIDUE MG E 2605
10
BC1
SOFTWARE
HOH F:800 , NAD F:6502
BINDING SITE FOR RESIDUE MG F 2606
11
BC2
SOFTWARE
HOH G:1247 , NAD G:7502
BINDING SITE FOR RESIDUE MG G 2607
12
BC3
SOFTWARE
NAD H:8502 , HOH H:8589
BINDING SITE FOR RESIDUE MG H 2608
13
BC4
SOFTWARE
VAL E:40 , ASP E:109 , GLN E:196
BINDING SITE FOR RESIDUE NA E 2705
14
BC5
SOFTWARE
THR F:39 , VAL F:40 , ASP F:109 , GLN F:196
BINDING SITE FOR RESIDUE NA F 2706
15
BC6
SOFTWARE
THR G:39 , VAL G:40 , ASP G:109 , GLN G:196
BINDING SITE FOR RESIDUE NA G 2707
16
BC7
SOFTWARE
THR H:39 , VAL H:40 , ASP H:109 , GLN H:196
BINDING SITE FOR RESIDUE NA H 2708
17
BC8
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 , THR A:244 , GLY A:245 , SER A:246 , ILE A:249 , ILE A:253 , GLU A:268 , LEU A:269 , GLY A:270 , CYS A:302 , GLN A:349 , GLU A:399 , PHE A:401 , LEU A:427 , PHE A:465 , MG A:2601 , HOH A:2817 , HOH A:2823
BINDING SITE FOR RESIDUE NAD A 1502
18
BC9
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 , PRO B:226 , GLY B:229 , ALA B:230 , PHE B:243 , THR B:244 , GLY B:245 , SER B:246 , ILE B:249 , ILE B:253 , GLU B:268 , LEU B:269 , GLY B:270 , CYS B:302 , GLN B:349 , GLU B:399 , PHE B:401 , LEU B:427 , MG B:2602 , HOH B:2720 , HOH B:2760 , HOH B:2762 , HOH B:2829
BINDING SITE FOR RESIDUE NAD B 2502
19
CC1
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 , GLY C:225 , PRO C:226 , GLY C:229 , ALA C:230 , PHE C:243 , THR C:244 , GLY C:245 , SER C:246 , ILE C:249 , ILE C:253 , GLU C:268 , LEU C:269 , GLY C:270 , CYS C:302 , GLN C:349 , GLU C:399 , MG C:2603 , HOH C:3564 , HOH C:3649 , HOH C:3667 , HOH C:3692
BINDING SITE FOR RESIDUE NAD C 3502
20
CC2
SOFTWARE
ILE D:165 , ILE D:166 , PRO D:167 , TRP D:168 , ASN D:169 , LYS D:192 , ALA D:194 , GLU D:195 , GLN D:196 , GLY D:225 , GLY D:229 , ALA D:230 , PHE D:243 , THR D:244 , GLY D:245 , SER D:246 , ILE D:249 , ILE D:253 , GLU D:268 , LEU D:269 , GLY D:270 , CYS D:302 , GLN D:349 , LYS D:352 , GLU D:399 , MG D:2604 , HOH D:4549 , HOH D:4674
BINDING SITE FOR RESIDUE NAD D 4502
21
CC3
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 , THR E:244 , GLY E:245 , SER E:246 , ILE E:249 , ILE E:253 , GLU E:268 , LEU E:269 , GLY E:270 , CYS E:302 , GLN E:349 , GLU E:399 , PHE E:401 , HOH E:851 , HOH E:852 , HOH E:854 , HOH E:1082 , MG E:2605
BINDING SITE FOR RESIDUE NAD E 5502
22
CC4
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 , GLY F:229 , ALA F:230 , PHE F:243 , THR F:244 , GLY F:245 , SER F:246 , ILE F:249 , ILE F:253 , GLU F:268 , LEU F:269 , GLY F:270 , CYS F:302 , GLN F:349 , GLU F:399 , PHE F:401 , HOH F:800 , HOH F:801 , HOH F:809 , HOH F:1033 , HOH F:1644 , MG F:2606
BINDING SITE FOR RESIDUE NAD F 6502
23
CC5
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 , GLN G:196 , GLY G:225 , GLY G:229 , ALA G:230 , PHE G:243 , THR G:244 , GLY G:245 , SER G:246 , ILE G:249 , ILE G:253 , GLU G:268 , LEU G:269 , GLY G:270 , CYS G:302 , GLN G:349 , GLU G:399 , PHE G:401 , HOH G:1247 , HOH G:1248 , HOH G:1259 , MG G:2607
BINDING SITE FOR RESIDUE NAD G 7502
24
CC6
SOFTWARE
ILE H:165 , ILE H:166 , PRO H:167 , TRP H:168 , ASN H:169 , LYS H:192 , GLU H:195 , GLN H:196 , GLY H:225 , GLY H:229 , ALA H:230 , PHE H:243 , THR H:244 , GLY H:245 , SER H:246 , ILE H:249 , ILE H:253 , GLU H:268 , LEU H:269 , GLY H:270 , CYS H:302 , GLN H:349 , GLU H:399 , PHE H:401 , LEU H:427 , MG H:2608 , HOH H:8590 , HOH H:8678
BINDING SITE FOR RESIDUE NAD H 8502
[
close Site info
]
SAPs(SNPs)/Variants
(3, 24)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_011869 (E320V, chain A/B/C/D/E/F/G/H, )
2: VAR_011302 (E479K, chain A/B/C/D/E/F/G/H, )
3: VAR_002248 (E487K, chain A/B/C/D/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
A/B/C/D/E/F/G/H
E
320
V
2
UniProt
VAR_011302
E
496
K
ALDH2_HUMAN
Polymorphism
---
A/B/C/D/E/F/G/H
E
479
K
3
UniProt
VAR_002248
E
504
K
ALDH2_HUMAN
Polymorphism
671
A/B/C/D/E/F/G/H
E
487
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 16)
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:
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
8
A:267-274
B:267-274
C:267-274
D:267-274
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
8
A:295-306
B:295-306
C:295-306
D:295-306
E:295-306
F:295-306
G:295-306
H:295-306
[
close PROSITE info
]
Exons
(13, 104)
Info
All Exons
Exon 1.1 (A:7-21 | B:7-21 | C:7-21 | D:7-21 ...)
Exon 1.2 (A:22-56 | B:22-56 | C:22-56 | D:22...)
Exon 1.3 (A:57-103 | B:57-103 | C:57-103 | D...)
Exon 1.4 (A:104-130 | B:104-130 | C:104-130 ...)
Exon 1.5 (A:130-167 | B:130-167 | C:130-167 ...)
Exon 1.6 (A:168-210 | B:168-210 | C:168-210 ...)
Exon 1.7 (A:211-248 | B:211-248 | C:211-248 ...)
Exon 1.8 (A:249-283 | B:249-283 | C:249-283 ...)
Exon 1.9 (A:283-344 | B:283-344 | C:283-344 ...)
Exon 1.10 (A:345-399 | B:345-399 | C:345-399 ...)
Exon 1.11 (A:400-452 | B:400-452 | C:400-452 ...)
Exon 1.12 (A:452-490 | B:452-490 | C:452-490 ...)
Exon 1.13 (A:491-500 | B:491-500 | C:491-500 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8
09: Boundary 1.8/1.9
10: Boundary 1.9/1.10
11: Boundary 1.10/1.11
12: Boundary 1.11/1.12
13: Boundary 1.12/1.13
14: Boundary 1.13/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000261733
1
ENSE00001297894
chr12:
112204346-112204900
555
ALDH2_HUMAN
1-38
38
8
A:7-21
B:7-21
C:7-21
D:7-21
E:7-21
F:7-21
G:7-21
H:7-21
15
15
15
15
15
15
15
15
1.2
ENST00000261733
2
ENSE00001302483
chr12:
112219722-112219826
105
ALDH2_HUMAN
39-73
35
8
A:22-56
B:22-56
C:22-56
D:22-56
E:22-56
F:22-56
G:22-56
H:22-56
35
35
35
35
35
35
35
35
1.3
ENST00000261733
3
ENSE00000755216
chr12:
112220962-112221102
141
ALDH2_HUMAN
74-120
47
8
A:57-103
B:57-103
C:57-103
D:57-103
E:57-103
F:57-103
G:57-103
H:57-103
47
47
47
47
47
47
47
47
1.4
ENST00000261733
4
ENSE00000755217
chr12:
112223071-112223150
80
ALDH2_HUMAN
121-147
27
8
A:104-130
B:104-130
C:104-130
D:104-130
E:104-130
F:104-130
G:104-130
H:104-130
27
27
27
27
27
27
27
27
1.5
ENST00000261733
5
ENSE00000755218
chr12:
112227627-112227738
112
ALDH2_HUMAN
147-184
38
8
A:130-167
B:130-167
C:130-167
D:130-167
E:130-167
F:130-167
G:130-167
H:130-167
38
38
38
38
38
38
38
38
1.6
ENST00000261733
6
ENSE00001316176
chr12:
112228238-112228366
129
ALDH2_HUMAN
185-227
43
8
A:168-210
B:168-210
C:168-210
D:168-210
E:168-210
F:168-210
G:168-210
H:168-210
43
43
43
43
43
43
43
43
1.7
ENST00000261733
7
ENSE00000755220
chr12:
112229110-112229223
114
ALDH2_HUMAN
228-265
38
8
A:211-248
B:211-248
C:211-248
D:211-248
E:211-248
F:211-248
G:211-248
H:211-248
38
38
38
38
38
38
38
38
1.8
ENST00000261733
8
ENSE00000755221
chr12:
112229865-112229967
103
ALDH2_HUMAN
266-300
35
8
A:249-283
B:249-283
C:249-283
D:249-283
E:249-283
F:249-283
G:249-283
H:249-283
35
35
35
35
35
35
35
35
1.9
ENST00000261733
9
ENSE00000755222
chr12:
112230402-112230586
185
ALDH2_HUMAN
300-361
62
8
A:283-344
B:283-344
C:283-344
D:283-344
E:283-344
F:283-344
G:283-344
H:283-344
62
62
62
62
62
62
62
62
1.10
ENST00000261733
10
ENSE00000755223
chr12:
112235882-112236046
165
ALDH2_HUMAN
362-416
55
8
A:345-399
B:345-399
C:345-399
D:345-399
E:345-399
F:345-399
G:345-399
H:345-399
55
55
55
55
55
55
55
55
1.11
ENST00000261733
11
ENSE00000755233
chr12:
112237710-112237867
158
ALDH2_HUMAN
417-469
53
8
A:400-452
B:400-452
C:400-452
D:400-452
E:400-452
F:400-452
G:400-452
H:400-452
53
53
53
53
53
53
53
53
1.12
ENST00000261733
12
ENSE00001304774
chr12:
112241663-112241777
115
ALDH2_HUMAN
469-507
39
8
A:452-490
B:452-490
C:452-490
D:452-490
E:452-490
F:452-490
G:452-490
H:452-490
39
39
39
39
39
39
39
39
1.13
ENST00000261733
13
ENSE00001129780
chr12:
112247347-112247782
436
ALDH2_HUMAN
508-517
10
8
A:491-500
B:491-500
C:491-500
D:491-500
E:491-500
F:491-500
G:491-500
H:491-500
10
10
10
10
10
10
10
10
[
close EXON info
]
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d1o00a_ (A:)
1b: SCOP_d1o00b_ (B:)
1c: SCOP_d1o00c_ (C:)
1d: SCOP_d1o00d_ (D:)
1e: SCOP_d1o00e_ (E:)
1f: SCOP_d1o00f_ (F:)
1g: SCOP_d1o00g_ (G:)
1h: SCOP_d1o00h_ (H:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
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
d1o00a_
A:
1b
d1o00b_
B:
1c
d1o00c_
C:
1d
d1o00d_
D:
1e
d1o00e_
E:
1f
d1o00f_
F:
1g
d1o00g_
G:
1h
d1o00h_
H:
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_1o00A01 (A:8-270,A:461-500)
1b: CATH_1o00B01 (B:8-270,B:461-500)
1c: CATH_1o00C01 (C:8-270,C:461-500)
1d: CATH_1o00D01 (D:8-270,D:461-500)
1e: CATH_1o00E01 (E:8-270,E:461-500)
1f: CATH_1o00F01 (F:8-270,F:461-500)
1g: CATH_1o00G01 (G:8-270,G:461-500)
1h: CATH_1o00H01 (H:8-270,H:461-500)
2a: CATH_1o00A02 (A:271-460)
2b: CATH_1o00B02 (B:271-460)
2c: CATH_1o00C02 (C:271-460)
2d: CATH_1o00D02 (D:271-460)
2e: CATH_1o00E02 (E:271-460)
2f: CATH_1o00F02 (F:271-460)
2g: CATH_1o00G02 (G:271-460)
2h: CATH_1o00H02 (H:271-460)
View:
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Label:
Classes
(
)
(
)
Architectures
(
)
(
)
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
1o00A01
A:8-270,A:461-500
1b
1o00B01
B:8-270,B:461-500
1c
1o00C01
C:8-270,C:461-500
1d
1o00D01
D:8-270,D:461-500
1e
1o00E01
E:8-270,E:461-500
1f
1o00F01
F:8-270,F:461-500
1g
1o00G01
G:8-270,G:461-500
1h
1o00H01
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
1o00A02
A:271-460
2b
1o00B02
B:271-460
2c
1o00C02
C:271-460
2d
1o00D02
D:271-460
2e
1o00E02
E:271-460
2f
1o00F02
F:271-460
2g
1o00G02
G:271-460
2h
1o00H02
H:271-460
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Aldedh_1o00H01 (H:28-491)
1b: PFAM_Aldedh_1o00H02 (H:28-491)
1c: PFAM_Aldedh_1o00H03 (H:28-491)
1d: PFAM_Aldedh_1o00H04 (H:28-491)
1e: PFAM_Aldedh_1o00H05 (H:28-491)
1f: PFAM_Aldedh_1o00H06 (H:28-491)
1g: PFAM_Aldedh_1o00H07 (H:28-491)
1h: PFAM_Aldedh_1o00H08 (H:28-491)
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Clan
:
ALDH-like
(49)
Family
:
Aldedh
(45)
Homo sapiens (Human)
(21)
1a
Aldedh-1o00H01
H:28-491
1b
Aldedh-1o00H02
H:28-491
1c
Aldedh-1o00H03
H:28-491
1d
Aldedh-1o00H04
H:28-491
1e
Aldedh-1o00H05
H:28-491
1f
Aldedh-1o00H06
H:28-491
1g
Aldedh-1o00H07
H:28-491
1h
Aldedh-1o00H08
H:28-491
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