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1NZX
Biol. Unit 2
Info
Asym.Unit (646 KB)
Biol.Unit 1 (322 KB)
Biol.Unit 2 (324 KB)
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(1)
Title
:
HUMAN MITOCHONDRIAL ALDEHYDE DEHYDROGENASE COMPLEXED WITH NAD+ IN THE PRESENCE OF LOW 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
:
2.45
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:
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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
(1, 4)
Info
All Hetero Components
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
2c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
2d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
2e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
2f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
2g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
2h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
1a: SODIUM ION (NAa)
1b: SODIUM ION (NAb)
1c: SODIUM ION (NAc)
1d: SODIUM ION (NAd)
2e: SODIUM ION (NAe)
2f: SODIUM ION (NAf)
2g: SODIUM ION (NAg)
2h: SODIUM ION (NAh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NA
-1
Ligand/Ion
SODIUM ION
2
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
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Sites
(8, 8)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
5: BC4 (SOFTWARE)
6: BC5 (SOFTWARE)
7: BC6 (SOFTWARE)
8: BC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
THR E:39 , VAL E:40 , ASP E:109 , GLN E:196
BINDING SITE FOR RESIDUE NA E 1705
2
AC6
SOFTWARE
THR F:39 , VAL F:40 , ASP F:109 , GLN F:196
BINDING SITE FOR RESIDUE NA F 1706
3
AC7
SOFTWARE
THR G:39 , VAL G:40 , ASP G:109 , GLN G:196
BINDING SITE FOR RESIDUE NA G 1707
4
AC8
SOFTWARE
THR H:39 , VAL H:40 , ASP H:109 , GLN H:196
BINDING SITE FOR RESIDUE NA H 1708
5
BC4
SOFTWARE
ILE E:165 , ILE E:166 , TRP E:168 , LYS E:192 , GLY E:225 , GLY E:229 , ALA E:230 , PHE E:243 , GLY E:245 , SER E:246 , ILE E:249 , HOH E:5575
BINDING SITE FOR RESIDUE NAD E 5502
6
BC5
SOFTWARE
ILE F:165 , ILE F:166 , TRP F:168 , LYS F:192 , GLU F:195 , GLY F:225 , GLY F:229 , ALA F:230 , PHE F:243 , SER F:246 , ILE F:249 , ILE F:253 , HOH F:6684 , HOH F:6716
BINDING SITE FOR RESIDUE NAD F 6502
7
BC6
SOFTWARE
ILE G:165 , ILE G:166 , TRP G:168 , LYS G:192 , GLY G:225 , GLY G:229 , ALA G:230 , PHE G:243 , SER G:246 , ILE G:249 , ILE G:253 , HOH G:7560
BINDING SITE FOR RESIDUE NAD G 7502
8
BC7
SOFTWARE
ILE H:165 , ILE H:166 , PRO H:167 , TRP H:168 , LYS H:192 , GLU H:195 , GLY H:225 , GLY H:229 , ALA H:230 , PHE H:243 , GLY H:245 , SER H:246 , ILE H:249
BINDING SITE FOR RESIDUE NAD H 8502
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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 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)
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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...)
;
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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
-
-
-
-
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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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_d1nzxa_ (A:)
1b: SCOP_d1nzxb_ (B:)
1c: SCOP_d1nzxc_ (C:)
1d: SCOP_d1nzxd_ (D:)
1e: SCOP_d1nzxe_ (E:)
1f: SCOP_d1nzxf_ (F:)
1g: SCOP_d1nzxg_ (G:)
1h: SCOP_d1nzxh_ (H:)
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Protein Domains
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Organisms
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(
)
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
d1nzxa_
A:
1b
d1nzxb_
B:
1c
d1nzxc_
C:
1d
d1nzxd_
D:
1e
d1nzxe_
E:
1f
d1nzxf_
F:
1g
d1nzxg_
G:
1h
d1nzxh_
H:
[
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CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_1nzxA01 (A:8-270,A:461-500)
1b: CATH_1nzxB01 (B:8-270,B:461-500)
1c: CATH_1nzxC01 (C:8-270,C:461-500)
1d: CATH_1nzxD01 (D:8-270,D:461-500)
1e: CATH_1nzxE01 (E:8-270,E:461-500)
1f: CATH_1nzxF01 (F:8-270,F:461-500)
1g: CATH_1nzxG01 (G:8-270,G:461-500)
1h: CATH_1nzxH01 (H:8-270,H:461-500)
2a: CATH_1nzxA02 (A:271-460)
2b: CATH_1nzxB02 (B:271-460)
2c: CATH_1nzxC02 (C:271-460)
2d: CATH_1nzxD02 (D:271-460)
2e: CATH_1nzxE02 (E:271-460)
2f: CATH_1nzxF02 (F:271-460)
2g: CATH_1nzxG02 (G:271-460)
2h: CATH_1nzxH02 (H:271-460)
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)
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)
(
)
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
1nzxA01
A:8-270,A:461-500
1b
1nzxB01
B:8-270,B:461-500
1c
1nzxC01
C:8-270,C:461-500
1d
1nzxD01
D:8-270,D:461-500
1e
1nzxE01
E:8-270,E:461-500
1f
1nzxF01
F:8-270,F:461-500
1g
1nzxG01
G:8-270,G:461-500
1h
1nzxH01
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
1nzxA02
A:271-460
2b
1nzxB02
B:271-460
2c
1nzxC02
C:271-460
2d
1nzxD02
D:271-460
2e
1nzxE02
E:271-460
2f
1nzxF02
F:271-460
2g
1nzxG02
G:271-460
2h
1nzxH02
H:271-460
[
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Aldedh_1nzxH01 (H:28-491)
1b: PFAM_Aldedh_1nzxH02 (H:28-491)
1c: PFAM_Aldedh_1nzxH03 (H:28-491)
1d: PFAM_Aldedh_1nzxH04 (H:28-491)
1e: PFAM_Aldedh_1nzxH05 (H:28-491)
1f: PFAM_Aldedh_1nzxH06 (H:28-491)
1g: PFAM_Aldedh_1nzxH07 (H:28-491)
1h: PFAM_Aldedh_1nzxH08 (H:28-491)
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Clans
(
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(
)
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(
)
Organisms
(
)
(
)
Clan
:
ALDH-like
(49)
Family
:
Aldedh
(45)
Homo sapiens (Human)
(21)
1a
Aldedh-1nzxH01
H:28-491
1b
Aldedh-1nzxH02
H:28-491
1c
Aldedh-1nzxH03
H:28-491
1d
Aldedh-1nzxH04
H:28-491
1e
Aldedh-1nzxH05
H:28-491
1f
Aldedh-1nzxH06
H:28-491
1g
Aldedh-1nzxH07
H:28-491
1h
Aldedh-1nzxH08
H:28-491
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