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3N80
Biol. Unit 1
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, 32)
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
10
Ligand/Ion
GUANIDINE
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
NA
-1
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(35, 35)
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)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: FC4 (SOFTWARE)
33: FC5 (SOFTWARE)
34: GC5 (SOFTWARE)
35: GC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:157 , PRO A:158 , VAL A:159 , HOH A:618 , HOH A:619 , TYR B:468
BINDING SITE FOR RESIDUE GAI A 801
02
AC2
SOFTWARE
ILE A:146 , ASP A:147 , PHE A:150 , HOH A:1033 , HOH A:1034 , VAL B:458 , PHE B:459
BINDING SITE FOR RESIDUE GAI A 811
03
AC3
SOFTWARE
PHE A:459 , HOH A:708 , HOH A:1119 , ILE B:146 , ASP B:147 , PHE B:150
BINDING SITE FOR RESIDUE GAI A 812
04
AC4
SOFTWARE
TYR A:153 , ARG A:155 , SER B:443 , PHE D:151
BINDING SITE FOR RESIDUE EDO A 901
05
AC5
SOFTWARE
HIS A:140 , GLY A:141 , LYS A:142 , HIS D:140 , GLY D:141 , LYS D:142
BINDING SITE FOR RESIDUE EDO A 910
06
AC6
SOFTWARE
GLN A:14 , ASN A:41 , THR A:44 , GLU A:46 , LEU A:108
BINDING SITE FOR RESIDUE EDO A 911
07
AC7
SOFTWARE
PHE A:18 , TYR A:101 , TYR A:203 , HOH A:522 , HOH A:525
BINDING SITE FOR RESIDUE EDO A 921
08
AC8
SOFTWARE
TYR A:441 , GLN A:444 , ALA A:445 , HOH A:519 , HOH A:549 , LEU B:72 , GLN C:497
BINDING SITE FOR RESIDUE EDO A 941
09
AC9
SOFTWARE
THR B:39 , VAL B:40 , ASP B:109 , GLN B:196 , HOH B:578 , HOH B:1635
BINDING SITE FOR RESIDUE NA B 602
10
BC1
SOFTWARE
TYR A:468 , PHE B:70 , GLU B:157 , PRO B:158 , VAL B:159 , HOH B:1309 , HOH B:1316
BINDING SITE FOR RESIDUE GAI B 802
11
BC2
SOFTWARE
SER A:443 , TYR B:153 , ARG B:155 , HOH B:1318 , PHE C:151
BINDING SITE FOR RESIDUE EDO B 902
12
BC3
SOFTWARE
HIS B:140 , GLY B:141 , LYS B:142 , HIS C:140 , GLY C:141 , LYS C:142
BINDING SITE FOR RESIDUE EDO B 909
13
BC4
SOFTWARE
GLN B:14 , ASN B:41 , THR B:44 , LEU B:108 , HOH B:1439
BINDING SITE FOR RESIDUE EDO B 912
14
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
15
BC6
SOFTWARE
TYR B:441 , GLN B:444 , ALA B:445 , HOH B:519 , HOH B:748 , GLN D:497
BINDING SITE FOR RESIDUE EDO B 942
16
BC7
SOFTWARE
THR C:39 , VAL C:40 , ASP C:109 , GLN C:196 , HOH C:606
BINDING SITE FOR RESIDUE NA C 603
17
BC8
SOFTWARE
GLU C:157 , PRO C:158 , VAL C:159 , HOH C:616 , HOH C:617 , TYR D:468
BINDING SITE FOR RESIDUE GAI C 803
18
BC9
SOFTWARE
ILE C:146 , ASP C:147 , PHE C:150 , HOH C:506 , PHE D:459
BINDING SITE FOR RESIDUE GAI C 813
19
CC1
SOFTWARE
PHE C:350 , ILE C:373 , ALA C:375 , ASP C:376 , GLY C:378 , EDO C:963 , HOH C:4557
BINDING SITE FOR RESIDUE GAI C 823
20
CC2
SOFTWARE
PHE B:151 , TYR C:153 , ARG C:155 , HOH C:1555 , SER D:443
BINDING SITE FOR RESIDUE EDO C 903
21
CC3
SOFTWARE
ASN C:41 , THR C:44 , LEU C:108 , HOH C:954 , HOH C:955
BINDING SITE FOR RESIDUE EDO C 913
22
CC4
SOFTWARE
PHE C:18 , TYR C:101 , TYR C:203 , HOH C:1751 , HOH C:4659
BINDING SITE FOR RESIDUE EDO C 923
23
CC5
SOFTWARE
GLN A:497 , TYR C:441 , GLN C:444 , ALA C:445 , HOH C:597 , HOH C:1399 , LEU D:72
BINDING SITE FOR RESIDUE EDO C 943
24
CC6
SOFTWARE
GLU C:347 , PHE C:350 , GAI C:823 , HOH C:4557 , GLY F:45
BINDING SITE FOR RESIDUE EDO C 963
25
CC7
SOFTWARE
THR D:39 , VAL D:40 , ASP D:109 , GLN D:196 , HOH D:3100
BINDING SITE FOR RESIDUE NA D 604
26
CC8
SOFTWARE
TYR C:468 , GLU D:157 , PRO D:158 , VAL D:159 , HOH D:746 , HOH D:756
BINDING SITE FOR RESIDUE GAI D 804
27
CC9
SOFTWARE
PHE C:459 , ILE D:146 , ASP D:147 , PHE D:150 , HOH D:728 , HOH D:1790
BINDING SITE FOR RESIDUE GAI D 814
28
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
29
DC2
SOFTWARE
PHE A:151 , SER C:443 , TYR D:153 , ARG D:155 , HOH D:3044
BINDING SITE FOR RESIDUE EDO D 904
30
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
31
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
32
FC4
SOFTWARE
HOH B:3215 , ALA F:68 , SER F:74 , HOH F:2437
BINDING SITE FOR RESIDUE EDO F 956
33
FC5
SOFTWARE
GLY C:45 , GLU F:347 , GAI F:826 , HOH F:2504
BINDING SITE FOR RESIDUE EDO F 966
34
GC5
SOFTWARE
HOH D:502 , THR H:36 , HOH H:1976 , HOH H:1978 , HOH H:1979
BINDING SITE FOR RESIDUE MG H 609
35
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
[
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:
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
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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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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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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Asym.Unit (730 KB)
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