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1MP0
Asym. Unit
Info
Asym.Unit (135 KB)
Biol.Unit 1 (129 KB)
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Title
:
BINARY COMPLEX OF HUMAN GLUTATHIONE-DEPENDENT FORMALDEHYDE DEHYDROGENASE WITH NAD(H)
Authors
:
P. C. Sanghani, H. Robinson, T. D. Hurley, W. F. Bosron
Date
:
10 Sep 02 (Deposition) - 25 Sep 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Glutathione Dependent Formaldehyde Dehydrogenase, Class Iii Alcohol Dehydrogenase, Mad, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. C. Sanghani, H. Robinson, R. Bennett-Lovsey, T. D. Hurley, W. F. Bosron
Structure-Function Relationships In Human Class Iii Alcohol Dehydrogenase (Formaldehyde Dehydrogenase)
Chem. Biol. Interact. V. 143 195 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 11)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
2
Ligand/Ion
POTASSIUM ION
2
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
PO4
3
Ligand/Ion
PHOSPHATE ION
4
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:96 , CYS A:99 , CYS A:102 , CYS A:110
BINDING SITE FOR RESIDUE ZN A 375
02
AC2
SOFTWARE
CYS A:44 , HIS A:66 , GLU A:67 , CYS A:173 , ARG A:368
BINDING SITE FOR RESIDUE ZN A 376
03
AC3
SOFTWARE
CYS B:96 , CYS B:99 , CYS B:102 , CYS B:110
BINDING SITE FOR RESIDUE ZN B 375
04
AC4
SOFTWARE
CYS B:44 , HIS B:66 , GLU B:67 , CYS B:173 , ARG B:368 , HOH B:804
BINDING SITE FOR RESIDUE ZN B 376
05
AC5
SOFTWARE
ALA A:186 , LYS A:187 , GLU A:189 , TYR A:263 , HOH A:985 , HOH A:1087
BINDING SITE FOR RESIDUE K A 701
06
AC6
SOFTWARE
HOH A:995 , ALA B:186 , LYS B:187 , GLU B:189 , TYR B:263 , HOH B:1000 , HOH B:1032
BINDING SITE FOR RESIDUE K B 702
07
AC7
SOFTWARE
LYS A:314 , HOH A:1036 , HOH A:1087 , LYS B:314
BINDING SITE FOR RESIDUE PO4 A 801
08
AC8
SOFTWARE
PO4 A:803 , LYS B:83 , LYS B:158 , HOH B:992 , HOH B:1008
BINDING SITE FOR RESIDUE PO4 B 802
09
AC9
SOFTWARE
LYS A:83 , LYS A:158 , HOH A:876 , HOH A:1092 , LYS B:83 , PO4 B:802
BINDING SITE FOR RESIDUE PO4 A 803
10
BC1
SOFTWARE
HIS A:45 , THR A:177 , GLY A:198 , GLY A:200 , GLY A:201 , VAL A:202 , ASP A:222 , ILE A:223 , CYS A:267 , ILE A:268 , VAL A:273 , VAL A:291 , GLY A:292 , VAL A:293 , THR A:316 , ALA A:317 , PHE A:318 , ARG A:368 , HOH A:813 , HOH A:822 , HOH A:829 , HOH A:834 , HOH A:836 , HOH A:838 , HOH A:873 , HOH A:888 , HOH A:933 , HOH A:972 , HOH A:980 , HOH A:1063 , HOH A:1097 , HOH A:1108
BINDING SITE FOR RESIDUE NAD A 777
11
BC2
SOFTWARE
HIS B:45 , CYS B:173 , THR B:177 , GLY B:198 , GLY B:200 , GLY B:201 , VAL B:202 , ASP B:222 , ILE B:223 , LYS B:227 , CYS B:267 , ILE B:268 , VAL B:291 , GLY B:292 , VAL B:293 , THR B:316 , ALA B:317 , PHE B:318 , ARG B:368 , HOH B:822 , HOH B:829 , HOH B:842 , HOH B:854 , HOH B:857 , HOH B:865 , HOH B:946 , HOH B:957 , HOH B:988 , HOH B:990 , HOH B:1002 , HOH B:1020 , HOH B:1114
BINDING SITE FOR RESIDUE NAD B 778
[
close Site info
]
SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_025823 (L162S, chain A/B, )
2: VAR_025824 (V308I, chain A/B, )
3: VAR_048199 (D352E, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_025823
L
163
S
ADHX_HUMAN
Polymorphism
28730623
A/B
L
162
S
2
UniProt
VAR_025824
V
309
I
ADHX_HUMAN
Polymorphism
28730628
A/B
V
308
I
3
UniProt
VAR_048199
D
353
E
ADHX_HUMAN
Polymorphism
16996593
A/B
D
352
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: ADH_ZINC (A:65-79,B:65-79)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADH_ZINC
PS00059
Zinc-containing alcohol dehydrogenases signature.
ADHX_HUMAN
66-80
2
A:65-79
B:65-79
[
close PROSITE info
]
Exons
(9, 18)
Info
All Exons
Exon 1.1c (A:114-187 | B:114-187)
Exon 1.2c (A:188-274 | B:188-274)
Exon 1.3a (A:275-320 | B:275-320)
Exon 1.4a (A:320-366 | B:320-366)
Exon 1.4c (A:366-373 | B:366-373)
Exon 1.5b (A:1-3 | B:1-3)
Exon 1.7 (A:4-37 | B:4-37)
Exon 1.8b (A:38-85 | B:38-85)
Exon 1.9a (A:85-114 | B:85-114)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1c
02: Boundary 1.1c/1.2c
03: Boundary 1.2c/1.3a
04: Boundary 1.3a/1.4a
05: Boundary 1.4a/1.4c
06: Boundary 1.4c/1.5b
07: Boundary 1.5b/1.7
08: Boundary 1.7/1.8b
09: Boundary 1.8b/1.9a
10: Boundary 1.9a/-
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
1.1c
ENST00000296412
1c
ENSE00001080657
chr4:
99998074-99997855
220
ADHX_HUMAN
115-188
74
2
A:114-187
B:114-187
74
74
1.2c
ENST00000296412
2c
ENSE00002174161
chr4:
99997703-99997443
261
ADHX_HUMAN
189-275
87
2
A:188-274
B:188-274
87
87
1.3a
ENST00000296412
3a
ENSE00001309047
chr4:
99996200-99996065
136
ADHX_HUMAN
276-321
46
2
A:275-320
B:275-320
46
46
1.4a
ENST00000296412
4a
ENSE00001134769
chr4:
99993862-99993724
139
ADHX_HUMAN
321-367
47
2
A:320-366
B:320-366
47
47
1.4c
ENST00000296412
4c
ENSE00001080651
chr4:
99993592-99992132
1461
ADHX_HUMAN
367-374
8
2
A:366-373
B:366-373
8
8
1.5b
ENST00000296412
5b
ENSE00002019192
chr4:
100009902-100009840
63
ADHX_HUMAN
1-4
4
2
A:1-3
B:1-3
3
3
1.7
ENST00000296412
7
ENSE00001670857
chr4:
100006367-100006266
102
ADHX_HUMAN
5-38
34
2
A:4-37
B:4-37
34
34
1.8b
ENST00000296412
8b
ENSE00001134723
chr4:
100003267-100003126
142
ADHX_HUMAN
39-86
48
2
A:38-85
B:38-85
48
48
1.9a
ENST00000296412
9a
ENSE00001080654
chr4:
100002603-100002516
88
ADHX_HUMAN
86-115
30
2
A:85-114
B:85-114
30
30
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1mp0a1 (A:1-162,A:339-373)
1b: SCOP_d1mp0b1 (B:1-162,B:339-373)
2a: SCOP_d1mp0a2 (A:163-338)
2b: SCOP_d1mp0b2 (B:163-338)
View:
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)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
GroES-like
(132)
Superfamily
:
GroES-like
(130)
Family
:
Alcohol dehydrogenase-like, N-terminal domain
(114)
Protein domain
:
Alcohol dehydrogenase
(77)
Human (Homo sapiens), different isozymes [TaxId: 9606]
(24)
1a
d1mp0a1
A:1-162,A:339-373
1b
d1mp0b1
B:1-162,B:339-373
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Alcohol dehydrogenase-like, C-terminal domain
(115)
Protein domain
:
Alcohol dehydrogenase
(77)
Human (Homo sapiens), different isozymes [TaxId: 9606]
(24)
2a
d1mp0a2
A:163-338
2b
d1mp0b2
B:163-338
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1mp0A02 (A:178-316)
1b: CATH_1mp0B02 (B:178-316)
2a: CATH_1mp0A01 (A:1-177,A:317-373)
2b: CATH_1mp0B01 (B:1-177,B:317-373)
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)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
1a
1mp0A02
A:178-316
1b
1mp0B02
B:178-316
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Quinone Oxidoreductase; Chain A, domain 1
(131)
Homologous Superfamily
:
Medium-chain alcohol dehydrogenases, catalytic domain
(131)
Human (Homo sapiens)
(30)
2a
1mp0A01
A:1-177,A:317-373
2b
1mp0B01
B:1-177,B:317-373
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_ADH_N_1mp0B01 (B:31-159)
1b: PFAM_ADH_N_1mp0B02 (B:31-159)
2a: PFAM_ADH_zinc_N_1mp0B03 (B:201-335)
2b: PFAM_ADH_zinc_N_1mp0B04 (B:201-335)
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GroES
(70)
Family
:
ADH_N
(62)
Homo sapiens (Human)
(18)
1a
ADH_N-1mp0B01
B:31-159
1b
ADH_N-1mp0B02
B:31-159
Clan
:
NADP_Rossmann
(1239)
Family
:
ADH_zinc_N
(75)
Homo sapiens (Human)
(24)
2a
ADH_zinc_N-1mp0B03
B:201-335
2b
ADH_zinc_N-1mp0B04
B:201-335
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