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2IA6
Asym. Unit
Info
Asym.Unit (155 KB)
Biol.Unit 1 (75 KB)
Biol.Unit 2 (77 KB)
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(1)
Title
:
BYPASS OF MAJOR BENZOPYRENE-DG ADDUCT BY Y-FAMILY DNA POLYMERASE WITH UNIQUE STRUCTURAL GAP
Authors
:
J. Bauer, H. Ling, J. M. Sayer, G. Xing, H. Yagi, D. M. Jerina
Date
:
07 Sep 06 (Deposition) - 11 Sep 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,C,D (1x)
Biol. Unit 2: B,E,F (1x)
Keywords
:
Benzo Pyrene, Carcinogen, Lesion Bypass, Polymerase, Translesion Synthesis, Dpo4, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Bauer, G. Xing, H. Yagi, J. M. Sayer, D. M. Jerina, H. Ling
A Structural Gap In Dpo4 Supports Mutagenic Bypass Of A Major Benzo[A]Pyrene Dg Adduct In Dna Through Template Misalignment.
Proc. Natl. Acad. Sci. Usa V. 104 14905 2007
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Hetero Components
(6, 18)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2a: 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDR... (BAPa)
2b: 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDR... (BAPb)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
3c: CALCIUM ION (CAc)
3d: CALCIUM ION (CAd)
3e: CALCIUM ION (CAe)
4a: 1,2-ETHANEDIOL (EDOa)
4b: 1,2-ETHANEDIOL (EDOb)
4c: 1,2-ETHANEDIOL (EDOc)
4d: 1,2-ETHANEDIOL (EDOd)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
6a: PHOSPHATE ION (PO4a)
6b: PHOSPHATE ION (PO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
2
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
BAP
2
Ligand/Ion
1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE
3
CA
5
Ligand/Ion
CALCIUM ION
4
EDO
4
Ligand/Ion
1,2-ETHANEDIOL
5
GOL
3
Ligand/Ion
GLYCEROL
6
PO4
2
Ligand/Ion
PHOSPHATE ION
[
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Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH C:441 , EDO C:607 , DG C:1805 , DA C:1806
BINDING SITE FOR RESIDUE EDO C 605
02
AC2
SOFTWARE
SER A:40 , GLY A:41 , ARG A:331 , PO4 A:1920
BINDING SITE FOR RESIDUE PO4 A 1919
03
AC3
SOFTWARE
HOH C:302 , HOH C:383 , HOH C:384 , DG C:1803 , DG C:1804
BINDING SITE FOR RESIDUE EDO C 606
04
AC4
SOFTWARE
PO4 A:1919
BINDING SITE FOR RESIDUE PO4 A 1920
05
AC5
SOFTWARE
HOH C:441 , EDO C:605 , DG C:1804 , DC D:1915 , DC D:1916
BINDING SITE FOR RESIDUE EDO C 607
06
AC6
SOFTWARE
HOH A:560 , DT C:1812 , DA C:1813 , DG D:1906 , DA D:1907
BINDING SITE FOR RESIDUE BAP D 2906
07
AC7
SOFTWARE
HOH E:271 , HOH E:436 , DG E:1804
BINDING SITE FOR RESIDUE GOL E 601
08
AC8
SOFTWARE
GLU B:271 , TYR B:274 , LYS B:275 , HOH B:649 , HOH B:772 , HOH F:443 , HOH F:445 , DG F:1906
BINDING SITE FOR RESIDUE BAP F 2906
09
AC9
SOFTWARE
DA E:1807 , HOH F:298 , HOH F:396 , DT F:1913 , DC F:1914
BINDING SITE FOR RESIDUE EDO F 602
10
BC1
SOFTWARE
HOH E:341 , DG E:1802 , DG E:1803 , HOH F:200 , DC F:1917 , DC F:1918
BINDING SITE FOR RESIDUE GOL F 604
11
BC2
SOFTWARE
ASP A:7 , PHE A:8 , ASP A:105 , ATP A:401 , HOH A:564
BINDING SITE FOR RESIDUE CA A 403
12
BC3
SOFTWARE
ALA A:181 , ILE A:186 , HOH A:421 , HOH A:548
BINDING SITE FOR RESIDUE CA A 404
13
BC4
SOFTWARE
ASP A:7 , PHE A:8 , TYR A:10 , PHE A:11 , THR A:45 , TYR A:48 , ARG A:51 , ALA A:57 , GLY A:58 , ASP A:105 , LYS A:159 , CA A:403 , HOH A:406 , HOH A:490 , HOH A:563 , HOH A:564 , HOH C:448 , DA C:1813 , HOH D:442
BINDING SITE FOR RESIDUE ATP A 401
14
BC5
SOFTWARE
ASP B:7 , PHE B:8 , ASP B:105 , ATP B:501
BINDING SITE FOR RESIDUE CA B 502
15
BC6
SOFTWARE
ASP B:7 , GLU B:106 , LYS B:152 , ATP B:501 , HOH B:756 , DA E:1813
BINDING SITE FOR RESIDUE CA B 503
16
BC7
SOFTWARE
ALA B:181 , ILE B:186 , HOH B:757 , HOH B:771 , HOH E:21 , HOH E:158
BINDING SITE FOR RESIDUE CA B 504
17
BC8
SOFTWARE
ASP B:7 , PHE B:8 , TYR B:10 , PHE B:11 , TYR B:12 , ALA B:44 , THR B:45 , TYR B:48 , ARG B:51 , ASP B:105 , LYS B:159 , CA B:502 , CA B:503 , HOH B:623 , HOH B:756 , DA E:1813 , DT F:1905
BINDING SITE FOR RESIDUE ATP B 501
18
BC9
SOFTWARE
GLY B:185 , HOH B:723 , HOH B:767
BINDING SITE FOR RESIDUE GOL B 603
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: UMUC (A:3-187,B:3-187)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UMUC
PS50173
UmuC domain profile.
DPO4_SULSO
3-187
2
A:3-187
B:3-187
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2ia6a2 (A:241-341)
1b: SCOP_d2ia6b2 (B:241-341)
2a: SCOP_d2ia6a1 (A:1-240)
2b: SCOP_d2ia6b1 (B:1-240)
View:
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Folds
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(
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(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Lesion bypass DNA polymerase (Y-family), little finger domain
(103)
Superfamily
:
Lesion bypass DNA polymerase (Y-family), little finger domain
(103)
Family
:
Lesion bypass DNA polymerase (Y-family), little finger domain
(62)
Protein domain
:
DinB homolog (DBH)
(39)
Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287]
(34)
1a
d2ia6a2
A:241-341
1b
d2ia6b2
B:241-341
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
Lesion bypass DNA polymerase (Y-family), catalytic domain
(104)
Protein domain
:
DinB homolog (DBH)
(46)
Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287]
(40)
2a
d2ia6a1
A:1-240
2b
d2ia6b1
B:1-240
[
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_2ia6A01 (A:2-10,A:78-166)
1b: CATH_2ia6B01 (B:2-10,B:78-166)
2a: CATH_2ia6A04 (A:244-341)
2b: CATH_2ia6B04 (B:244-341)
3a: CATH_2ia6A03 (A:167-233)
3b: CATH_2ia6B03 (B:167-233)
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Topologies
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Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.270, no name defined]
(278)
Sulfolobus solfataricus. Organism_taxid: 273057. Strain: p2.
(1)
1a
2ia6A01
A:2-10,A:78-166
1b
2ia6B01
B:2-10,B:78-166
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
[code=3.30.1490.100, no name defined]
(80)
Sulfolobus solfataricus. Organism_taxid: 273057. Strain: p2.
(1)
2a
2ia6A04
A:244-341
2b
2ia6B04
B:244-341
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
Sulfolobus solfataricus. Organism_taxid: 273057. Strain: p2.
(1)
3a
2ia6A03
A:167-233
3b
2ia6B03
B:167-233
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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Atom Selection
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Chain E
Chain F
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