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2OXM
Asym. Unit
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Asym.Unit (51 KB)
Biol.Unit 1 (47 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A UNG2/MODIFIED DNA COMPLEX THAT REPRESENT A STABILIZED SHORT-LIVED EXTRAHELICAL STATE IN EZYMATIC DNA BASE FLIPPING
Authors
:
M. A. Bianchet, D. J. Krosky, Stivers J. T. , L. M. Amzel
Date
:
20 Feb 07 (Deposition) - 30 Oct 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Enzyme Dna Complex, Ung2, Uracil Dna Glycosylase, Hydrolase/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. B. Parker, M. A. Bianchet, D. J. Krosky, J. I. Friedman, L. M. Amzel, J. T. Stivers
Enzymatic Capture Of An Extrahelical Thymine In The Search For Uracil In Dna.
Nature V. 449 433 2007
(for further references see the
PDB file header
)
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: 1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ER... (4MFa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
4MF
1
Mod. Nucleotide
1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-4-METHYL-1H-INDOLE
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:91 , TYR A:275 , HOH A:370 , DT B:4 , DT C:26 , DA C:28
BINDING SITE FOR RESIDUE 4MF C 27
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_017094 (F242S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_017094
F
251
S
UNG_HUMAN
Disease (HIGM5)
---
A
F
242
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: U_DNA_GLYCOSYLASE (A:138-147)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
U_DNA_GLYCOSYLASE
PS00130
Uracil-DNA glycosylase signature.
UNG_HUMAN
147-156
1
A:138-147
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Exons
(6, 6)
Info
All Exons
Exon 1.2c (A:82-104)
Exon 1.3 (A:105-136)
Exon 1.4 (A:137-169)
Exon 1.5 (A:169-199)
Exon 1.6 (A:199-258)
Exon 1.7 (A:259-304)
View:
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All Exon Boundaries
1: Boundary 1.1/1.2c
2: Boundary 1.2c/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7
7: Boundary 1.7/-
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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
1.1
ENST00000242576
1
ENSE00001130047
chr12:
109535415-109535616
202
UNG_HUMAN
1-44
44
0
-
-
1.2c
ENST00000242576
2c
ENSE00001130067
chr12:
109536237-109536443
207
UNG_HUMAN
45-113
69
1
A:82-104
23
1.3
ENST00000242576
3
ENSE00000754701
chr12:
109536994-109537089
96
UNG_HUMAN
114-145
32
1
A:105-136
32
1.4
ENST00000242576
4
ENSE00000754703
chr12:
109539707-109539804
98
UNG_HUMAN
146-178
33
1
A:137-169
33
1.5
ENST00000242576
5
ENSE00000754705
chr12:
109540644-109540732
89
UNG_HUMAN
178-208
31
1
A:169-199
31
1.6
ENST00000242576
6
ENSE00000834681
chr12:
109541238-109541416
179
UNG_HUMAN
208-267
60
1
A:199-258
60
1.7
ENST00000242576
7
ENSE00001130061
chr12:
109547634-109548798
1165
UNG_HUMAN
268-313
46
1
A:259-304
46
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2oxma_ (A:)
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(
)
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)
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)
(
)
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Uracil-DNA glycosylase-like
(59)
Superfamily
:
Uracil-DNA glycosylase-like
(59)
Family
:
Uracil-DNA glycosylase
(37)
Protein domain
:
Uracil-DNA glycosylase
(32)
Human (Homo sapiens) [TaxId: 9606]
(14)
1a
d2oxma_
A:
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2oxmA00 (A:82-304)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Uracil-DNA Glycosylase, subunit E
(52)
Homologous Superfamily
:
Uracil-DNA Glycosylase, subunit E
(52)
Human (Homo sapiens)
(10)
1a
2oxmA00
A:82-304
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Pfam Domains
(0, 0)
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all PFAM domains
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