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3N80
Biol. Unit 2
Info
Asym.Unit (730 KB)
Biol.Unit 1 (364 KB)
Biol.Unit 2 (367 KB)
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(1)
Title
:
HUMAN MITOCHONDRIAL ALDEHYDE DEHYDROGENASE, APO FORM
Authors
:
L. Gonzalez-Segura, T. D. Hurley
Date
:
27 May 10 (Deposition) - 13 Apr 11 (Release) - 13 Apr 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
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
:
Oxidoreductase, Aldh, Rossmann Fold
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. -K. Ho, L. Gonzalez-Segura, S. Perez-Miller, H. Weiner, T. D. Hurle
Conformational Selection During Catalysis: The Role Of Threonine 244 In Aldh2
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 33)
Info
All Hetero Components
1a: S-HYDROXYCYSTEINE (CSOa)
1b: S-HYDROXYCYSTEINE (CSOb)
1c: S-HYDROXYCYSTEINE (CSOc)
1d: S-HYDROXYCYSTEINE (CSOd)
1e: S-HYDROXYCYSTEINE (CSOe)
1f: S-HYDROXYCYSTEINE (CSOf)
1g: S-HYDROXYCYSTEINE (CSOg)
1h: S-HYDROXYCYSTEINE (CSOh)
2a: 1,2-ETHANEDIOL (EDOa)
2aa: 1,2-ETHANEDIOL (EDOaa)
2ab: 1,2-ETHANEDIOL (EDOab)
2ac: 1,2-ETHANEDIOL (EDOac)
2ad: 1,2-ETHANEDIOL (EDOad)
2ae: 1,2-ETHANEDIOL (EDOae)
2af: 1,2-ETHANEDIOL (EDOaf)
2ag: 1,2-ETHANEDIOL (EDOag)
2ah: 1,2-ETHANEDIOL (EDOah)
2ai: 1,2-ETHANEDIOL (EDOai)
2aj: 1,2-ETHANEDIOL (EDOaj)
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)
2z: 1,2-ETHANEDIOL (EDOz)
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)
3j: GUANIDINE (GAIj)
3k: GUANIDINE (GAIk)
3l: GUANIDINE (GAIl)
3m: GUANIDINE (GAIm)
3n: GUANIDINE (GAIn)
3o: GUANIDINE (GAIo)
3p: GUANIDINE (GAIp)
3q: GUANIDINE (GAIq)
3r: GUANIDINE (GAIr)
3s: GUANIDINE (GAIs)
3t: GUANIDINE (GAIt)
3u: GUANIDINE (GAIu)
4a: MAGNESIUM ION (MGa)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
5d: SODIUM ION (NAd)
5e: SODIUM ION (NAe)
5f: SODIUM ION (NAf)
5g: SODIUM ION (NAg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CSO
4
Mod. Amino Acid
S-HYDROXYCYSTEINE
2
EDO
18
Ligand/Ion
1,2-ETHANEDIOL
3
GAI
11
Ligand/Ion
GUANIDINE
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
NA
-1
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(39, 39)
Info
All Sites
01: BC5 (SOFTWARE)
02: CC6 (SOFTWARE)
03: DC1 (SOFTWARE)
04: DC3 (SOFTWARE)
05: DC4 (SOFTWARE)
06: DC5 (SOFTWARE)
07: DC6 (SOFTWARE)
08: DC7 (SOFTWARE)
09: DC8 (SOFTWARE)
10: DC9 (SOFTWARE)
11: EC1 (SOFTWARE)
12: EC2 (SOFTWARE)
13: EC3 (SOFTWARE)
14: EC4 (SOFTWARE)
15: EC5 (SOFTWARE)
16: EC6 (SOFTWARE)
17: EC7 (SOFTWARE)
18: EC8 (SOFTWARE)
19: EC9 (SOFTWARE)
20: FC1 (SOFTWARE)
21: FC2 (SOFTWARE)
22: FC3 (SOFTWARE)
23: FC4 (SOFTWARE)
24: FC5 (SOFTWARE)
25: FC6 (SOFTWARE)
26: FC7 (SOFTWARE)
27: FC8 (SOFTWARE)
28: FC9 (SOFTWARE)
29: GC1 (SOFTWARE)
30: GC2 (SOFTWARE)
31: GC3 (SOFTWARE)
32: GC4 (SOFTWARE)
33: GC5 (SOFTWARE)
34: GC6 (SOFTWARE)
35: GC7 (SOFTWARE)
36: GC8 (SOFTWARE)
37: GC9 (SOFTWARE)
38: HC1 (SOFTWARE)
39: HC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC5
SOFTWARE
ARG B:97 , ASP B:98 , THR B:100 , TYR B:101 , HOH B:1464 , HOH B:1466 , ALA E:7 , HOH E:3463 , HOH E:4303
BINDING SITE FOR RESIDUE EDO B 922
02
CC6
SOFTWARE
GLU C:347 , PHE C:350 , GAI C:823 , HOH C:4557 , GLY F:45
BINDING SITE FOR RESIDUE EDO C 963
03
DC1
SOFTWARE
GLN D:14 , PRO D:15 , LEU D:108 , HOH D:507 , HOH D:508 , HOH D:509 , HOH H:3296
BINDING SITE FOR RESIDUE GAI D 833
04
DC3
SOFTWARE
ASN D:41 , THR D:44 , GLU D:46 , HOH D:508 , HOH D:509 , GLU H:46
BINDING SITE FOR RESIDUE EDO D 914
05
DC4
SOFTWARE
GLU D:414 , TYR D:441 , HOH D:611 , HOH D:658 , HOH D:1158 , LYS G:361
BINDING SITE FOR RESIDUE EDO D 944
06
DC5
SOFTWARE
THR E:39 , VAL E:40 , ASP E:109 , GLN E:196 , HOH E:3502
BINDING SITE FOR RESIDUE NA E 605
07
DC6
SOFTWARE
PHE E:70 , GLU E:157 , PRO E:158 , VAL E:159 , HOH E:4095 , TYR F:468
BINDING SITE FOR RESIDUE GAI E 805
08
DC7
SOFTWARE
ILE E:146 , ASP E:147 , PHE E:150 , HOH E:2116 , PHE F:459 , HOH F:2775
BINDING SITE FOR RESIDUE GAI E 815
09
DC8
SOFTWARE
TYR E:153 , ARG E:155 , HOH E:4165 , SER F:443 , PHE H:151
BINDING SITE FOR RESIDUE EDO E 905
10
DC9
SOFTWARE
GLN E:14 , ASN E:41 , THR E:44 , GLU E:46 , LEU E:108
BINDING SITE FOR RESIDUE EDO E 915
11
EC1
SOFTWARE
HIS E:140 , GLY E:141 , LYS E:142 , HIS H:140 , GLY H:141 , LYS H:142
BINDING SITE FOR RESIDUE EDO E 920
12
EC2
SOFTWARE
PHE E:18 , TYR E:101 , TYR E:203 , HOH E:3469
BINDING SITE FOR RESIDUE EDO E 925
13
EC3
SOFTWARE
THR F:39 , VAL F:40 , ASP F:109 , GLN F:196 , HOH F:3832
BINDING SITE FOR RESIDUE NA F 606
14
EC4
SOFTWARE
TYR E:468 , GLU F:157 , PRO F:158 , VAL F:159 , HOH F:3882 , HOH F:3883
BINDING SITE FOR RESIDUE GAI F 806
15
EC5
SOFTWARE
PHE E:459 , HOH E:4299 , ILE F:146 , ASP F:147 , PHE F:150 , HOH F:2347
BINDING SITE FOR RESIDUE GAI F 816
16
EC6
SOFTWARE
PHE F:350 , ILE F:373 , ALA F:375 , ASP F:376 , GLY F:378 , EDO F:966 , HOH F:2504
BINDING SITE FOR RESIDUE GAI F 826
17
EC7
SOFTWARE
ALA F:326 , LYS F:327 , ARG F:329 , VAL F:331 , PRO F:383 , HOH F:2185 , HOH F:2186 , HOH F:4668 , HOH F:4795
BINDING SITE FOR RESIDUE GAI F 839
18
EC8
SOFTWARE
SER E:443 , TYR F:153 , ARG F:155 , HOH F:3874 , PHE G:151
BINDING SITE FOR RESIDUE EDO F 906
19
EC9
SOFTWARE
ASN F:41 , THR F:44 , GLU F:46 , LEU F:108 , HOH F:2489 , HOH F:2490
BINDING SITE FOR RESIDUE EDO F 916
20
FC1
SOFTWARE
HIS F:140 , GLY F:141 , LYS F:142 , HIS G:140 , GLY G:141 , LYS G:142
BINDING SITE FOR RESIDUE EDO F 919
21
FC2
SOFTWARE
ARG E:321 , HOH E:3393 , HOH E:3394 , TYR F:101 , TYR F:203 , HOH F:2173 , HOH F:3848
BINDING SITE FOR RESIDUE EDO F 926
22
FC3
SOFTWARE
LEU E:72 , TYR F:441 , GLN F:444 , ALA F:445 , HOH F:2734 , HOH F:2735 , GLN H:497
BINDING SITE FOR RESIDUE EDO F 946
23
FC4
SOFTWARE
HOH B:3215 , ALA F:68 , SER F:74 , HOH F:2437
BINDING SITE FOR RESIDUE EDO F 956
24
FC5
SOFTWARE
GLY C:45 , GLU F:347 , GAI F:826 , HOH F:2504
BINDING SITE FOR RESIDUE EDO F 966
25
FC6
SOFTWARE
THR G:39 , VAL G:40 , ASP G:109 , GLN G:196 , HOH G:2861
BINDING SITE FOR RESIDUE NA G 607
26
FC7
SOFTWARE
PHE G:70 , GLU G:157 , PRO G:158 , VAL G:159 , HOH G:2959 , HOH G:2960 , HOH G:4293 , TYR H:468
BINDING SITE FOR RESIDUE GAI G 807
27
FC8
SOFTWARE
ILE G:146 , ASP G:147 , PHE G:150 , HOH G:3741 , HOH G:3888 , VAL H:458 , PHE H:459
BINDING SITE FOR RESIDUE GAI G 817
28
FC9
SOFTWARE
ALA G:326 , LYS G:327 , ARG G:329 , PRO G:383 , HOH G:2832
BINDING SITE FOR RESIDUE GAI G 838
29
GC1
SOFTWARE
PHE F:151 , TYR G:153 , ARG G:155 , HOH G:3449 , SER H:443
BINDING SITE FOR RESIDUE EDO G 907
30
GC2
SOFTWARE
ASN G:41 , THR G:44 , GLU G:46
BINDING SITE FOR RESIDUE EDO G 917
31
GC3
SOFTWARE
PHE G:18 , TYR G:101 , TYR G:203 , HOH G:2647 , HOH G:2856
BINDING SITE FOR RESIDUE EDO G 927
32
GC4
SOFTWARE
THR H:39 , VAL H:40 , ASP H:109 , GLN H:196 , HOH H:4242 , HOH H:4243
BINDING SITE FOR RESIDUE NA H 608
33
GC5
SOFTWARE
HOH D:502 , THR H:36 , HOH H:1976 , HOH H:1978 , HOH H:1979
BINDING SITE FOR RESIDUE MG H 609
34
GC6
SOFTWARE
PHE H:70 , GLU H:157 , PRO H:158 , VAL H:159 , HOH H:3602 , HOH H:4209
BINDING SITE FOR RESIDUE GAI H 808
35
GC7
SOFTWARE
PHE G:459 , HOH G:4070 , ILE H:146 , ASP H:147 , PHE H:150
BINDING SITE FOR RESIDUE GAI H 818
36
GC8
SOFTWARE
PHE E:151 , SER G:443 , TYR H:153 , ARG H:155 , HOH H:3634
BINDING SITE FOR RESIDUE EDO H 908
37
GC9
SOFTWARE
GLU D:46 , ARG D:377 , ASN H:41 , THR H:44 , GLU H:46 , HOH H:3290 , HOH H:3292 , HOH H:3294
BINDING SITE FOR RESIDUE EDO H 918
38
HC1
SOFTWARE
LYS E:361 , HOH E:3327 , PHE H:18 , TYR H:101 , TYR H:203 , HOH H:2038
BINDING SITE FOR RESIDUE EDO H 928
39
HC2
SOFTWARE
GLN F:497 , LEU G:72 , TYR H:441 , GLN H:444 , ALA H:445 , HOH H:3409 , HOH H:4298
BINDING SITE FOR RESIDUE EDO H 948
[
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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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
-
-
-
-
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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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_d3n80a_ (A:)
1b: SCOP_d3n80c_ (C:)
1c: SCOP_d3n80d_ (D:)
1d: SCOP_d3n80e_ (E:)
1e: SCOP_d3n80f_ (F:)
1f: SCOP_d3n80g_ (G:)
1g: SCOP_d3n80h_ (H:)
1h: SCOP_d3n80b_ (B:)
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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
d3n80a_
A:
1b
d3n80c_
C:
1c
d3n80d_
D:
1d
d3n80e_
E:
1e
d3n80f_
F:
1f
d3n80g_
G:
1g
d3n80h_
H:
1h
d3n80b_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Aldedh_3n80H01 (H:28-491)
1b: PFAM_Aldedh_3n80H02 (H:28-491)
1c: PFAM_Aldedh_3n80H03 (H:28-491)
1d: PFAM_Aldedh_3n80H04 (H:28-491)
1e: PFAM_Aldedh_3n80H05 (H:28-491)
1f: PFAM_Aldedh_3n80H06 (H:28-491)
1g: PFAM_Aldedh_3n80H07 (H:28-491)
1h: PFAM_Aldedh_3n80H08 (H:28-491)
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
ALDH-like
(49)
Family
:
Aldedh
(45)
Homo sapiens (Human)
(21)
1a
Aldedh-3n80H01
H:28-491
1b
Aldedh-3n80H02
H:28-491
1c
Aldedh-3n80H03
H:28-491
1d
Aldedh-3n80H04
H:28-491
1e
Aldedh-3n80H05
H:28-491
1f
Aldedh-3n80H06
H:28-491
1g
Aldedh-3n80H07
H:28-491
1h
Aldedh-3n80H08
H:28-491
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