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1TEH
Asym. Unit
Info
Asym.Unit (122 KB)
Biol.Unit 1 (117 KB)
Biol.Unit 2 (115 KB)
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(1)
Title
:
STRUCTURE OF HUMAN LIVER CHICHI ALCOHOL DEHYDROGENASE (A GLUTATHIONE-DEPENDENT FORMALDEHYDE DEHYDROGENASE)
Authors
:
Z. -N. Yang, T. D. Hurley
Date
:
05 Feb 96 (Deposition) - 07 Dec 96 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (2x)
Biol. Unit 2: B (2x)
Keywords
:
Nad+ Dependent Alcohol Dehydrogenase Glutathione Dependent Formaldehyde Dehydrogenase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. N. Yang, W. F. Bosron, T. D. Hurley
Structure Of Human Chi Chi Alcohol Dehydrogenase: A Glutathione-Dependent Formaldehyde Dehydrogenase.
J. Mol. Biol. V. 265 330 1997
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 7)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2
ZN
5
Ligand/Ion
ZINC ION
[
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]
Sites
(12, 12)
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: ZN1 (UNKNOWN)
09: ZN2 (UNKNOWN)
10: ZN3 (UNKNOWN)
11: ZN4 (UNKNOWN)
12: ZNS (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:97 , CYS A:100 , CYS A:103 , CYS A:111
BINDING SITE FOR RESIDUE ZN A 375
02
AC2
SOFTWARE
CYS A:46 , HIS A:67 , GLU A:68 , CYS A:174
BINDING SITE FOR RESIDUE ZN A 376
03
AC3
SOFTWARE
CYS B:97 , GLY B:98 , CYS B:100 , CYS B:103 , CYS B:111
BINDING SITE FOR RESIDUE ZN B 375
04
AC4
SOFTWARE
CYS B:46 , HIS B:67 , GLU B:68 , CYS B:174 , ARG B:369
BINDING SITE FOR RESIDUE ZN B 376
05
AC5
SOFTWARE
GLU B:360 , HIS B:363
BINDING SITE FOR RESIDUE ZN B 378
06
AC6
SOFTWARE
HIS A:47 , TYR A:93 , THR A:178 , GLY A:202 , VAL A:203 , ASP A:223 , ILE A:224 , CYS A:268 , ILE A:269 , VAL A:274 , VAL A:292 , GLY A:293 , VAL A:294 , THR A:317 , ALA A:318 , PHE A:319 , ARG A:369 , HOH A:382
BINDING SITE FOR RESIDUE NAD A 377
07
AC7
SOFTWARE
HIS B:47 , THR B:178 , LEU B:200 , GLY B:201 , GLY B:202 , VAL B:203 , ASP B:223 , ILE B:224 , LYS B:228 , CYS B:268 , ILE B:269 , VAL B:274 , VAL B:292 , GLY B:293 , VAL B:294 , THR B:317 , PHE B:319 , ARG B:369
BINDING SITE FOR RESIDUE NAD B 377
08
ZN1
UNKNOWN
CYS A:97 , CYS A:100 , CYS A:103 , CYS A:111 , ZN A:375
ZNA1 IN CHITOPH19.ZNC AND CHIPARAM1.ZNC.
09
ZN2
UNKNOWN
CYS A:46 , HIS A:67 , GLU A:68 , CYS A:174 , HOH A:378 , ZN A:376
GLU 68 IS NEARLY-COORDINATED TO THE ZINC, 2.87 ANGSTROMS. HOH A401 IS 3.18 ANGSTROMS TO THE ZINC. ZNB IN CHITOPH19.ZNC AND CHIPARAM1.ZNC. ZNB IS SET TO BOND TO CYS 46, HIS 67 AND CYS 174 IN CHITOPH19.ZNC AND CHIPARAM1.ZNC.
10
ZN3
UNKNOWN
CYS B:97 , CYS B:100 , CYS B:103 , CYS B:111 , ZN B:375
ZNB1 IN CHITOPH19.ZNC AND CHIPARAM1.ZNC.
11
ZN4
UNKNOWN
CYS B:46 , HIS B:67 , GLU B:68 , CYS B:174 , ZN B:376
GLU 68 IS COORDINATED TO THE ZINC, 2.04 ANGSTROMS. ZNB IN CHITOPH19.ZNC AND CHIPARAM1.ZNC. ZNB IS SET TO BOND TO CYS 46, HIS 67 AND CYS 174 IN CHITOPH19.ZNC AND CHIPARAM1.ZNC.
12
ZNS
UNKNOWN
GLU B:360 , HIS B:363 , ZN B:378
THIS ZINC IS POSITIONED ON CRYSTALLOGRAPHIC X AXIS, THEREFORE ASSIGNED AN OCCUPANCY OF 0.5 IN ORDER TO BE REFINED AS SPECIAL POSITION ATOM IN XPLOR. THE OTHER TWO LIGANDS ARE HIS 360 AND GLU 363 FROM THE SYMMETRY COPIES. ZNS IS DEFINED IN CHITOPH19.ZNS AND CHIPARAM19.ZNS. IT IS NOT PRESET TO BOND WITH HIS AND GLU.
[
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]
SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_025823 (L163S, chain A/B, )
2: VAR_025824 (V309I, chain A/B, )
3: VAR_048199 (D353E, 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
163
S
2
UniProt
VAR_025824
V
309
I
ADHX_HUMAN
Polymorphism
28730628
A/B
V
309
I
3
UniProt
VAR_048199
D
353
E
ADHX_HUMAN
Polymorphism
16996593
A/B
D
353
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:66-80,B:66-80)
;
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:66-80
B:66-80
[
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]
Exons
(9, 18)
Info
All Exons
Exon 1.1c (A:115-188 | B:115-188)
Exon 1.2c (A:189-275 | B:189-275)
Exon 1.3a (A:276-321 | B:276-321)
Exon 1.4a (A:321-367 | B:321-367)
Exon 1.4c (A:367-374 | B:367-374)
Exon 1.5b (A:3-5 | B:3-5)
Exon 1.7 (A:6-39 | B:6-39)
Exon 1.8b (A:40-86 | B:40-86)
Exon 1.9a (A:86-115 | B:86-115)
View:
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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:
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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:115-188
B:115-188
74
74
1.2c
ENST00000296412
2c
ENSE00002174161
chr4:
99997703-99997443
261
ADHX_HUMAN
189-275
87
2
A:189-275
B:189-275
87
87
1.3a
ENST00000296412
3a
ENSE00001309047
chr4:
99996200-99996065
136
ADHX_HUMAN
276-321
46
2
A:276-321
B:276-321
46
46
1.4a
ENST00000296412
4a
ENSE00001134769
chr4:
99993862-99993724
139
ADHX_HUMAN
321-367
47
2
A:321-367
B:321-367
47
47
1.4c
ENST00000296412
4c
ENSE00001080651
chr4:
99993592-99992132
1461
ADHX_HUMAN
367-374
8
2
A:367-374
B:367-374
8
8
1.5b
ENST00000296412
5b
ENSE00002019192
chr4:
100009902-100009840
63
ADHX_HUMAN
1-4
4
2
A:3-5
B:3-5
3
3
1.7
ENST00000296412
7
ENSE00001670857
chr4:
100006367-100006266
102
ADHX_HUMAN
5-38
34
2
A:6-39
B:6-39
34
34
1.8b
ENST00000296412
8b
ENSE00001134723
chr4:
100003267-100003126
142
ADHX_HUMAN
39-86
48
2
A:40-86
B:40-86
48
48
1.9a
ENST00000296412
9a
ENSE00001080654
chr4:
100002603-100002516
88
ADHX_HUMAN
86-115
30
2
A:86-115
B:86-115
30
30
[
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]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1teha1 (A:3-162,A:339-374)
1b: SCOP_d1tehb1 (B:3-162,B:339-374)
2a: SCOP_d1teha2 (A:163-338)
2b: SCOP_d1tehb2 (B:163-338)
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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
d1teha1
A:3-162,A:339-374
1b
d1tehb1
B:3-162,B:339-374
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
d1teha2
A:163-338
2b
d1tehb2
B:163-338
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1tehA02 (A:179-317)
1b: CATH_1tehB02 (B:179-317)
2a: CATH_1tehA01 (A:3-178,A:318-374)
2b: CATH_1tehB01 (B:3-178,B:318-374)
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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
1tehA02
A:179-317
1b
1tehB02
B:179-317
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
1tehA01
A:3-178,A:318-374
2b
1tehB01
B:3-178,B:318-374
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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