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3SI8
Asym. Unit
Info
Asym.Unit (89 KB)
Biol.Unit 1 (83 KB)
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(1)
Title
:
HUMAN DNA POLYMERASE ETA - DNA TERNARY COMPLEX WITH THE 5'T OF A CPD IN THE ACTIVE SITE (TT2)
Authors
:
C. Biertumpfel, Y. Zhao, Y. Kondo, S. Ramon-Maiques, M. Gregory, J. Y. L C. Masutani, A. R. Lehmann, F. Hanaoka, W. Yang
Date
:
17 Jun 11 (Deposition) - 03 Aug 11 (Release) - 03 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,P,T
Biol. Unit 1: A,P,T (1x)
Keywords
:
Protein-Dna Complex, Multiple Domains, Three Are Alpha/Beta Fold And One Of The Four Is Helical Fold, Dna Polymerase, Dna Binding, Mg2+ And Dntp Binding, Affinity Tag Is Added And Partially Removed At The N-Terminal End, Nucleus, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Biertumpfel, Y. Zhao, Y. Kondo, S. Ramon-Maiques, M. Gregory, J. Y. Lee, C. Masutani, A. R. Lehmann, F. Hanaoka, W. Yang
Structure And Mechanism Of Human Dna Polymerase Eta.
Nature V. 465 1044 2010
[
close entry info
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Hetero Components
(8, 21)
Info
All Hetero Components
1a: (2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-Y... (3D1a)
2a: COBALT (II) ION (COa)
3a: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTa)
3b: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTb)
4a: 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HY... (DZ4a)
5a: 1,2-ETHANEDIOL (EDOa)
5b: 1,2-ETHANEDIOL (EDOb)
5c: 1,2-ETHANEDIOL (EDOc)
5d: 1,2-ETHANEDIOL (EDOd)
5e: 1,2-ETHANEDIOL (EDOe)
6a: GLYCEROL (GOLa)
6b: GLYCEROL (GOLb)
6c: GLYCEROL (GOLc)
6d: GLYCEROL (GOLd)
6e: GLYCEROL (GOLe)
6f: GLYCEROL (GOLf)
6g: GLYCEROL (GOLg)
6h: GLYCEROL (GOLh)
7a: MAGNESIUM ION (MGa)
7b: MAGNESIUM ION (MGb)
8a: CIS-SYN CYCLOBUTANE THYMINE DIMER (TTDa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3D1
1
Ligand/Ion
(2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2-(HYDROXYMETHYL)FURAN-3-OL
2
CO
1
Ligand/Ion
COBALT (II) ION
3
DTT
2
Ligand/Ion
2,3-DIHYDROXY-1,4-DITHIOBUTANE
4
DZ4
1
Ligand/Ion
2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE
5
EDO
5
Ligand/Ion
1,2-ETHANEDIOL
6
GOL
8
Ligand/Ion
GLYCEROL
7
MG
2
Ligand/Ion
MAGNESIUM ION
8
TTD
1
Mod. Nucleotide
CIS-SYN CYCLOBUTANE THYMINE DIMER
[
close Hetero Component info
]
Sites
(20, 20)
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)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:13 , MET A:14 , ASP A:15 , CYS A:16 , PHE A:17 , PHE A:18 , ALA A:49 , TYR A:52 , ARG A:55 , ARG A:61 , ASP A:115 , LYS A:231 , MG A:450 , MG A:451 , HOH A:475 , HOH A:495 , DA P:9 , TTD T:5
BINDING SITE FOR RESIDUE DZ4 A 433
02
AC2
SOFTWARE
HIS A:240 , GLY A:241 , PRO A:244 , EDO A:449
BINDING SITE FOR RESIDUE GOL A 434
03
AC3
SOFTWARE
THR A:282 , SER A:284 , HOH A:460
BINDING SITE FOR RESIDUE GOL A 435
04
AC4
SOFTWARE
THR A:353 , ASN A:357
BINDING SITE FOR RESIDUE GOL A 436
05
AC5
SOFTWARE
LEU A:11 , GLU A:116 , LYS A:224 , CYS A:227 , GLY A:228 , LYS A:231 , HOH A:495 , DA P:9
BINDING SITE FOR RESIDUE GOL A 437
06
AC6
SOFTWARE
SER A:257 , LEU A:262 , LYS A:293 , ASN A:294 , TRP A:297
BINDING SITE FOR RESIDUE 3D1 A 438
07
AC7
SOFTWARE
ASP A:181 , ASN A:182 , LEU A:183 , GLN A:280 , GLN A:285
BINDING SITE FOR RESIDUE GOL A 439
08
AC8
SOFTWARE
VAL A:372 , ASP A:375 , ARG A:377
BINDING SITE FOR RESIDUE GOL A 440
09
AC9
SOFTWARE
ASP A:140 , LYS A:168
BINDING SITE FOR RESIDUE GOL A 441
10
BC1
SOFTWARE
SER A:265 , HIS A:289 , PHE A:290 , GLN A:343 , GLN A:346 , EDO A:447
BINDING SITE FOR RESIDUE GOL A 442
11
BC2
SOFTWARE
GLN A:287 , GLY A:291 , GLU A:292 , GLU A:335 , TRP A:339
BINDING SITE FOR RESIDUE DTT A 443
12
BC3
SOFTWARE
GLU A:148 , GLY A:149 , TRP A:174 , SER A:239 , SER A:242 , EDO A:445
BINDING SITE FOR RESIDUE DTT A 444
13
BC4
SOFTWARE
GLN A:152 , SER A:177 , DTT A:444
BINDING SITE FOR RESIDUE EDO A 445
14
BC5
SOFTWARE
LYS A:224 , ARG A:253 , ARG A:256 , DT P:8 , DA P:9
BINDING SITE FOR RESIDUE EDO A 446
15
BC6
SOFTWARE
GOL A:442
BINDING SITE FOR RESIDUE EDO A 447
16
BC7
SOFTWARE
ARG A:253 , GLY A:260
BINDING SITE FOR RESIDUE EDO A 448
17
BC8
SOFTWARE
HIS A:240 , ARG A:303 , GOL A:434
BINDING SITE FOR RESIDUE EDO A 449
18
BC9
SOFTWARE
ASP A:13 , MET A:14 , ASP A:115 , DZ4 A:433 , MG A:451
BINDING SITE FOR RESIDUE MG A 450
19
CC1
SOFTWARE
ASP A:13 , ASP A:115 , GLU A:116 , DZ4 A:433 , MG A:450 , HOH A:495 , DA P:9
BINDING SITE FOR RESIDUE MG A 451
20
CC2
SOFTWARE
ASP A:181 , HIS A:289 , HIS A:393 , HIS A:397
BINDING SITE FOR RESIDUE CO A 452
[
close Site info
]
SAPs(SNPs)/Variants
(10, 10)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_070836 (R93P, chain A, )
02: VAR_021227 (R111H, chain A, )
03: VAR_021228 (T122P, chain A, )
04: VAR_036220 (G153D, chain A, )
05: VAR_021229 (G209V, chain A, )
06: VAR_021230 (G263V, chain A, )
07: VAR_070837 (V266D, chain A, )
08: VAR_070838 (G295R, chain A, )
09: VAR_021231 (R334W, chain A, )
10: VAR_021232 (R361S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_070836
R
93
P
POLH_HUMAN
Disease (XPV)
---
A
R
93
P
02
UniProt
VAR_021227
R
111
H
POLH_HUMAN
Disease (XPV)
---
A
R
111
H
03
UniProt
VAR_021228
T
122
P
POLH_HUMAN
Disease (XPV)
---
A
T
122
P
04
UniProt
VAR_036220
G
153
D
POLH_HUMAN
Unclassified
---
A
G
153
D
05
UniProt
VAR_021229
G
209
V
POLH_HUMAN
Polymorphism
2307456
A
G
209
V
06
UniProt
VAR_021230
G
263
V
POLH_HUMAN
Disease (XPV)
---
A
G
263
V
07
UniProt
VAR_070837
V
266
D
POLH_HUMAN
Disease (XPV)
---
A
V
266
D
08
UniProt
VAR_070838
G
295
R
POLH_HUMAN
Disease (XPV)
---
A
G
295
R
09
UniProt
VAR_021231
R
334
W
POLH_HUMAN
Polymorphism
9333548
A
R
334
W
10
UniProt
VAR_021232
R
361
S
POLH_HUMAN
Disease (XPV)
---
A
R
361
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: UMUC (A:9-259)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UMUC
PS50173
UmuC domain profile.
POLH_HUMAN
9-259
1
A:9-259
[
close PROSITE info
]
Exons
(10, 10)
Info
All Exons
Exon 1.2 (A:1-46)
Exon 1.3 (A:46-91)
Exon 1.4b (A:91-164 (gaps))
Exon 1.5 (A:164-220)
Exon 1.6 (A:221-255)
Exon 1.7 (A:255-295)
Exon 1.8 (A:295-336)
Exon 1.9 (A:337-358)
Exon 1.10 (A:359-415 (gaps))
Exon 1.11a (A:415-430)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.2
02: Boundary 1.2/1.3
03: Boundary 1.3/1.4b
04: Boundary 1.4b/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
10: Boundary 1.10/1.11a
11: Boundary 1.11a/-
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
ENST00000372236
1a
ENSE00001717994
chr6:
43543887-43544177
291
POLH_HUMAN
-
0
0
-
-
1.2
ENST00000372236
2
ENSE00001457304
chr6:
43550053-43550193
141
POLH_HUMAN
1-46
46
1
A:1-46
46
1.3
ENST00000372236
3
ENSE00002161294
chr6:
43550744-43550878
135
POLH_HUMAN
46-91
46
1
A:46-91
46
1.4b
ENST00000372236
4b
ENSE00000752927
chr6:
43555009-43555226
218
POLH_HUMAN
91-164
74
1
A:91-164 (gaps)
74
1.5
ENST00000372236
5
ENSE00000481500
chr6:
43565433-43565602
170
POLH_HUMAN
164-220
57
1
A:164-220
57
1.6
ENST00000372236
6
ENSE00001172213
chr6:
43568725-43568828
104
POLH_HUMAN
221-255
35
1
A:221-255
35
1.7
ENST00000372236
7
ENSE00001172207
chr6:
43571629-43571748
120
POLH_HUMAN
255-295
41
1
A:255-295
41
1.8
ENST00000372236
8
ENSE00001172201
chr6:
43572352-43572475
124
POLH_HUMAN
295-336
42
1
A:295-336
42
1.9
ENST00000372236
9
ENSE00001172195
chr6:
43572991-43573056
66
POLH_HUMAN
337-358
22
1
A:337-358
22
1.10
ENST00000372236
10
ENSE00001172191
chr6:
43578291-43578460
170
POLH_HUMAN
359-415
57
1
A:359-415 (gaps)
57
1.11a
ENST00000372236
11a
ENSE00001861041
chr6:
43581397-43583397
2001
POLH_HUMAN
415-713
299
1
A:415-430
16
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
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