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1U3U
Asym. Unit
Info
Asym.Unit (142 KB)
Biol.Unit 1 (137 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN ALCOHOL DEHYDROGENASE BETA-1-BETA-1 ISOFORM COMPLEXED WITH N-BENZYLFORMAMIDE DETERMINED TO 1.6 ANGSTROM RESOLUTION
Authors
:
B. J. Gibbons, T. D. Hurley
Date
:
23 Jul 04 (Deposition) - 26 Oct 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. J. Gibbons, T. D. Hurley
Structure Of Three Class I Human Alcohol Dehydrogenases Complexed With Isoenzyme Specific Formamide Inhibitors
Biochemistry V. 43 12555 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 9)
Info
All Hetero Components
1a: N-BENZYLFORMAMIDE (BNFa)
1b: N-BENZYLFORMAMIDE (BNFb)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3a: PHOSPHATE ION (PO4a)
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
BNF
2
Ligand/Ion
N-BENZYLFORMAMIDE
2
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
PO4
1
Ligand/Ion
PHOSPHATE ION
4
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:97 , CYS A:100 , CYS A:103 , CYS A:111
BINDING SITE FOR RESIDUE ZN A 375
2
AC2
SOFTWARE
CYS A:46 , HIS A:67 , CYS A:174 , NAD A:1377 , BNF A:1378
BINDING SITE FOR RESIDUE ZN A 376
3
AC3
SOFTWARE
CYS B:97 , CYS B:100 , CYS B:103 , CYS B:111
BINDING SITE FOR RESIDUE ZN B 375
4
AC4
SOFTWARE
CYS B:46 , HIS B:67 , CYS B:174 , NAD B:2377 , BNF B:2378
BINDING SITE FOR RESIDUE ZN B 376
5
AC5
SOFTWARE
SER A:1 , LYS A:5 , HOH A:1613 , HOH A:1725 , THR B:127 , ARG B:128 , HOH B:2483 , HOH B:2545 , HOH B:2817
BINDING SITE FOR RESIDUE PO4 B 400
6
AC6
SOFTWARE
ARG A:47 , THR A:48 , HIS A:51 , PHE A:93 , CYS A:174 , THR A:178 , GLY A:199 , LEU A:200 , GLY A:201 , GLY A:202 , VAL A:203 , ASP A:223 , ILE A:224 , LYS A:228 , VAL A:268 , ILE A:269 , ARG A:271 , VAL A:292 , GLY A:293 , VAL A:294 , ALA A:317 , VAL A:318 , TYR A:319 , LEU A:362 , ARG A:369 , ZN A:376 , BNF A:1378 , HOH A:1397 , HOH A:1413 , HOH A:1425 , HOH A:1426 , HOH A:1448 , HOH A:1471 , HOH A:1515 , HOH A:1719 , HOH A:1839
BINDING SITE FOR RESIDUE NAD A 1377
7
AC7
SOFTWARE
ARG B:47 , THR B:48 , HIS B:51 , PHE B:93 , CYS B:174 , THR B:178 , GLY B:199 , LEU B:200 , GLY B:201 , GLY B:202 , VAL B:203 , ASP B:223 , ILE B:224 , LYS B:228 , VAL B:268 , ILE B:269 , ARG B:271 , VAL B:292 , VAL B:294 , ALA B:317 , VAL B:318 , TYR B:319 , LEU B:362 , ARG B:369 , ZN B:376 , BNF B:2378 , HOH B:2428 , HOH B:2446 , HOH B:2470 , HOH B:2476 , HOH B:2491 , HOH B:2503 , HOH B:2579 , HOH B:2873
BINDING SITE FOR RESIDUE NAD B 2377
8
AC8
SOFTWARE
CYS A:46 , THR A:48 , HIS A:67 , PHE A:93 , CYS A:174 , ZN A:376 , NAD A:1377
BINDING SITE FOR RESIDUE BNF A 1378
9
AC9
SOFTWARE
CYS B:46 , THR B:48 , HIS B:67 , PHE B:93 , LEU B:116 , CYS B:174 , ZN B:376 , NAD B:2377
BINDING SITE FOR RESIDUE BNF B 2378
[
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]
SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_000426 (R47H, chain A/B, )
2: VAR_019322 (N56K, chain A/B, )
3: VAR_019323 (T59S, chain A/B, )
4: VAR_000427 (R369C, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_000426
R
48
H
ADH1B_HUMAN
Polymorphism
1229984
A/B
R
47
H
2
UniProt
VAR_019322
N
57
K
ADH1B_HUMAN
Polymorphism
1041969
A/B
N
56
K
3
UniProt
VAR_019323
T
60
S
ADH1B_HUMAN
Polymorphism
6413413
A/B
T
59
S
4
UniProt
VAR_000427
R
370
C
ADH1B_HUMAN
Polymorphism
2066702
A/B
R
369
C
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.
ADH1B_HUMAN
67-81
2
A:66-80
B:66-80
[
close PROSITE info
]
Exons
(9, 18)
Info
All Exons
Exon 1.1b (A:1-5 | B:1-5)
Exon 1.2c (A:6-39 | B:6-39)
Exon 1.3a (A:40-86 | B:40-86)
Exon 1.4b (A:86-115 | B:86-115)
Exon 1.5b (A:115-188 | B:115-188)
Exon 1.6 (A:189-275 | B:189-275)
Exon 1.7 (A:276-321 | B:276-321)
Exon 1.8 (A:321-367 | B:321-367)
Exon 1.9d (A:367-374 | B:367-374)
View:
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Label:
All Exon Boundaries
01: Boundary -/1.1b
02: Boundary 1.1b/1.2c
03: Boundary 1.2c/1.3a
04: Boundary 1.3a/1.4b
05: Boundary 1.4b/1.5b
06: Boundary 1.5b/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8
09: Boundary 1.8/1.9d
10: Boundary 1.9d/-
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
1.1b
ENST00000305046
1b
ENSE00001383360
chr4:
100242556-100242471
86
ADH1B_HUMAN
1-6
6
2
A:1-5
B:1-5
5
5
1.2c
ENST00000305046
2c
ENSE00001624682
chr4:
100240043-100239942
102
ADH1B_HUMAN
7-40
34
2
A:6-39
B:6-39
34
34
1.3a
ENST00000305046
3a
ENSE00001600077
chr4:
100239341-100239203
139
ADH1B_HUMAN
41-87
47
2
A:40-86
B:40-86
47
47
1.4b
ENST00000305046
4b
ENSE00001655834
chr4:
100237459-100237372
88
ADH1B_HUMAN
87-116
30
2
A:86-115
B:86-115
30
30
1.5b
ENST00000305046
5b
ENSE00001727418
chr4:
100237274-100237055
220
ADH1B_HUMAN
116-189
74
2
A:115-188
B:115-188
74
74
1.6
ENST00000305046
6
ENSE00001736990
chr4:
100235238-100234978
261
ADH1B_HUMAN
190-276
87
2
A:189-275
B:189-275
87
87
1.7
ENST00000305046
7
ENSE00001711573
chr4:
100232813-100232678
136
ADH1B_HUMAN
277-322
46
2
A:276-321
B:276-321
46
46
1.8
ENST00000305046
8
ENSE00001682168
chr4:
100232060-100231922
139
ADH1B_HUMAN
322-368
47
2
A:321-367
B:321-367
47
47
1.9d
ENST00000305046
9d
ENSE00002069705
chr4:
100229021-100226121
2901
ADH1B_HUMAN
368-375
8
2
A:367-374
B:367-374
8
8
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1u3ua1 (A:1-162,A:339-374)
1b: SCOP_d1u3ub1 (B:1-162,B:339-374)
2a: SCOP_d1u3ua2 (A:163-338)
2b: SCOP_d1u3ub2 (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
d1u3ua1
A:1-162,A:339-374
1b
d1u3ub1
B:1-162,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
d1u3ua2
A:163-338
2b
d1u3ub2
B:163-338
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1u3uA02 (A:179-317)
1b: CATH_1u3uB02 (B:179-317)
2a: CATH_1u3uA01 (A:1-178,A:318-374)
2b: CATH_1u3uB01 (B:1-178,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
1u3uA02
A:179-317
1b
1u3uB02
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
1u3uA01
A:1-178,A:318-374
2b
1u3uB01
B:1-178,B:318-374
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_ADH_N_1u3uB01 (B:33-160)
1b: PFAM_ADH_N_1u3uB02 (B:33-160)
2a: PFAM_ADH_zinc_N_1u3uB03 (B:202-334)
2b: PFAM_ADH_zinc_N_1u3uB04 (B:202-334)
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)
(
)
Families
(
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(
)
Organisms
(
)
(
)
Clan
:
GroES
(70)
Family
:
ADH_N
(62)
Homo sapiens (Human)
(18)
1a
ADH_N-1u3uB01
B:33-160
1b
ADH_N-1u3uB02
B:33-160
Clan
:
NADP_Rossmann
(1239)
Family
:
ADH_zinc_N
(75)
Homo sapiens (Human)
(24)
2a
ADH_zinc_N-1u3uB03
B:202-334
2b
ADH_zinc_N-1u3uB04
B:202-334
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