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2W7P
Asym. Unit
Info
Asym.Unit (175 KB)
Biol.Unit 1 (85 KB)
Biol.Unit 2 (84 KB)
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(1)
Title
:
STRUCTURE AND ACTIVITY OF BYPASS SYNTHESIS BY HUMAN DNA POLYMERASE KAPPA OPPOSITE THE 7,8-DIHYDRO-8-OXODEOXYGUANOSINE ADDUCT
Authors
:
A. Irimia, M. Egli
Date
:
23 Dec 08 (Deposition) - 16 Jun 09 (Release) - 25 Aug 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.71
Chains
:
Asym. Unit : A,B,E,F,P,T
Biol. Unit 1: A,P,T (1x)
Biol. Unit 2: B,E,F (1x)
Keywords
:
8-Oxo-2P-Deoxy-Guanosine-5P-Monophosphate, Translesion Dna Polymerase, Human Dna Polymerase Kappa, Datp, Dna Repair, Dna Damage, Dna-Binding Protein
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
A. Irimia, R. L. Eoff, F. P. Guengerich, M. Egli
Structural And Functional Elucidation Of The Mechanism Promoting Error-Prone Synthesis By Human Dna Polymerase Kappa Opposite The 7, 8-Dihydro-8- Oxo-2'-Deoxyguanosine Adduct.
J. Biol. Chem. V. 284 22467 2009
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Hetero Components
(3, 8)
Info
All Hetero Components
1a: 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPH... (8OGa)
1b: 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPH... (8OGb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPa)
3b: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
8OG
2
Mod. Nucleotide
8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2
CA
4
Ligand/Ion
CALCIUM ION
3
DTP
2
Ligand/Ion
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:107 , MET A:108 , ASP A:109 , ALA A:110 , SER A:137 , THR A:138 , TYR A:141 , ARG A:144 , ALA A:150 , ASP A:198 , ASP A:325 , LYS A:328 , CA A:1522 , CA A:1523 , DC P:13 , 8OG T:5
BINDING SITE FOR RESIDUE DTP A1521
2
AC2
SOFTWARE
ASP B:107 , ALA B:110 , SER B:137 , THR B:138 , ARG B:144 , ALA B:151 , ASP B:198 , ASP B:325 , LYS B:328 , CA B:1522 , CA B:1523 , DC E:13 , 8OG F:5
BINDING SITE FOR RESIDUE DTP B1521
3
AC3
SOFTWARE
ASP A:107 , ASP A:325 , DTP A:1521
BINDING SITE FOR RESIDUE CA A1522
4
AC4
SOFTWARE
ASP A:107 , MET A:108 , ASP A:198 , DTP A:1521
BINDING SITE FOR RESIDUE CA A1523
5
AC5
SOFTWARE
ASP B:107 , ASP B:325 , DTP B:1521
BINDING SITE FOR RESIDUE CA B1522
6
AC6
SOFTWARE
ASP B:107 , MET B:108 , ASP B:198 , DTP B:1521
BINDING SITE FOR RESIDUE CA B1523
[
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SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_048886 (S423R, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_048886
S
423
R
POLK_HUMAN
Polymorphism
35257416
A/B
S
423
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: UMUC (A:103-358,B:103-358)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UMUC
PS50173
UmuC domain profile.
POLK_HUMAN
103-358
2
A:103-358
B:103-358
[
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Exons
(12, 24)
Info
All Exons
Exon 1.4a (A:33-45 | B:33-45)
Exon 1.5b (A:46-85 | B:46-85)
Exon 1.7b (A:86-136 | B:86-136)
Exon 1.8b (A:137-180 | B:137-180)
Exon 1.9b (A:181-224 | B:181-223)
Exon 1.10a (A:282-312 | B:282-312)
Exon 1.11 (A:312-353 | B:312-353)
Exon 1.12 (A:354-409 | B:354-409)
Exon 1.13 (A:409-420 | B:409-420)
Exon 1.14a (A:420-452 | B:420-452)
Exon 1.15a (A:453-510 | B:453-510)
Exon 1.16a (A:510-521 | B:510-521)
View:
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All Exon Boundaries
01: Boundary 1.1a/1.4a
02: Boundary 1.4a/1.5b
03: Boundary 1.5b/1.7b
04: Boundary 1.7b/1.8b
05: Boundary 1.8b/1.9b
06: Boundary 1.9b/1.10a
07: Boundary 1.10a/1.11
08: Boundary 1.11/1.12
09: Boundary 1.12/1.13
10: Boundary 1.13/1.14a
11: Boundary 1.14a/1.15a
12: Boundary 1.15a/1.16a
13: Boundary 1.16a/1.17b
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
1.1a
ENST00000241436
1a
ENSE00002022143
chr5:
74807581-74807739
159
POLK_HUMAN
-
0
0
-
-
1.4a
ENST00000241436
4a
ENSE00002160720
chr5:
74842835-74842982
148
POLK_HUMAN
1-45
45
2
A:33-45
B:33-45
13
13
1.5b
ENST00000241436
5b
ENSE00001649227
chr5:
74848297-74848416
120
POLK_HUMAN
46-85
40
2
A:46-85
B:46-85
40
40
1.7b
ENST00000241436
7b
ENSE00001643362
chr5:
74865165-74865317
153
POLK_HUMAN
86-136
51
2
A:86-136
B:86-136
51
51
1.8b
ENST00000241436
8b
ENSE00000827223
chr5:
74869563-74869694
132
POLK_HUMAN
137-180
44
2
A:137-180
B:137-180
44
44
1.9b
ENST00000241436
9b
ENSE00000827224
chr5:
74872605-74872758
154
POLK_HUMAN
181-232
52
2
A:181-224
B:181-223
44
43
1.10a
ENST00000241436
10a
ENSE00000827225
chr5:
74877034-74877273
240
POLK_HUMAN
232-312
81
2
A:282-312
B:282-312
31
31
1.11
ENST00000241436
11
ENSE00000827226
chr5:
74879118-74879242
125
POLK_HUMAN
312-353
42
2
A:312-353
B:312-353
42
42
1.12
ENST00000241436
12
ENSE00000827227
chr5:
74880585-74880751
167
POLK_HUMAN
354-409
56
2
A:354-409
B:354-409
56
56
1.13
ENST00000241436
13
ENSE00001004825
chr5:
74882851-74882883
33
POLK_HUMAN
409-420
12
2
A:409-420
B:409-420
12
12
1.14a
ENST00000241436
14a
ENSE00000827228
chr5:
74886169-74886265
97
POLK_HUMAN
420-452
33
2
A:420-452
B:420-452
33
33
1.15a
ENST00000241436
15a
ENSE00000827229
chr5:
74889703-74889874
172
POLK_HUMAN
453-510
58
2
A:453-510
B:453-510
58
58
1.16a
ENST00000241436
16a
ENSE00001742078
chr5:
74892047-74893003
957
POLK_HUMAN
510-829
320
2
A:510-521
B:510-521
12
12
1.17b
ENST00000241436
17b
ENSE00001614437
chr5:
74893572-74893614
43
POLK_HUMAN
829-843
15
0
-
-
1.17l
ENST00000241436
17l
ENSE00001905813
chr5:
74893759-74896969
3211
POLK_HUMAN
843-870
28
0
-
-
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_IMS_HHH_2w7pB01 (B:339-370)
1b: PFAM_IMS_HHH_2w7pB02 (B:339-370)
2a: PFAM_IMS_2w7pB03 (B:106-325)
2b: PFAM_IMS_2w7pB04 (B:106-325)
3a: PFAM_IMS_C_2w7pB05 (B:381-510)
3b: PFAM_IMS_C_2w7pB06 (B:381-510)
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Clans
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)
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HHH
(112)
Family
:
IMS_HHH
(56)
Homo sapiens (Human)
(3)
1a
IMS_HHH-2w7pB01
B:339-370
1b
IMS_HHH-2w7pB02
B:339-370
Clan
:
no clan defined [family: IMS]
(76)
Family
:
IMS
(76)
Homo sapiens (Human)
(14)
2a
IMS-2w7pB03
B:106-325
2b
IMS-2w7pB04
B:106-325
Clan
:
no clan defined [family: IMS_C]
(74)
Family
:
IMS_C
(74)
Homo sapiens (Human)
(14)
3a
IMS_C-2w7pB05
B:381-510
3b
IMS_C-2w7pB06
B:381-510
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