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1S0M
Biol. Unit 1
Info
Asym.Unit (152 KB)
Biol.Unit 1 (75 KB)
Biol.Unit 2 (74 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCT IN A TERNARY COMPLEX WITH A DNA POLYMERASE
Authors
:
H. Ling, J. M. Sayer, F. Boudsocq, B. S. Plosky, R. Woodgate, W. Yang
Date
:
31 Dec 03 (Deposition) - 30 Mar 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
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, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Ling, J. M. Sayer, B. S. Plosky, H. Yagi, F. Boudsocq, R. Woodgate, D. M. Jerina, W. Yang
Crystal Structure Of A Benzo[A]Pyrene Diol Epoxide Adduct I A Ternary Complex With A Dna Polymerase.
Proc. Natl. Acad. Sci. Usa V. 101 2265 2004
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDR... (BAPa)
1b: 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDR... (BAPb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
2g: CALCIUM ION (CAg)
3a: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPa)
3b: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPb)
4a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BAP
1
Ligand/Ion
1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
DTP
1
Ligand/Ion
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
4
MG
-1
Ligand/Ion
MAGNESIUM ION
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC6 (SOFTWARE)
4: AC7 (SOFTWARE)
5: AC9 (SOFTWARE)
6: BC2 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:7 , ASP A:105 , GLU A:106 , DTP A:803 , HOH A:917
BINDING SITE FOR RESIDUE MG A 401
2
AC3
SOFTWARE
ASP A:7 , PHE A:8 , ASP A:105 , DTP A:803
BINDING SITE FOR RESIDUE CA A 402
3
AC6
SOFTWARE
ALA A:181 , ILE A:186 , HOH A:805 , HOH A:878 , HOH A:914 , HOH C:269
BINDING SITE FOR RESIDUE CA A 406
4
AC7
SOFTWARE
ASP A:294 , HOH A:873 , HOH A:875 , HOH A:908 , HOH A:913 , HOH C:127
BINDING SITE FOR RESIDUE CA A 407
5
AC9
SOFTWARE
DTP A:803 , HOH C:165 , DT C:1813 , HOH D:33 , DA D:1906
BINDING SITE FOR RESIDUE BAP D 1920
6
BC2
SOFTWARE
ASP A:7 , PHE A:8 , TYR A:10 , PHE A:11 , ALA A:44 , THR A:45 , ARG A:51 , ALA A:57 , GLY A:58 , ASP A:105 , LYS A:159 , MG A:401 , CA A:402 , HOH A:804 , HOH A:819 , HOH A:827 , HOH A:840 , HOH A:841 , HOH A:915 , HOH A:922 , DT D:1905 , BAP D:1920
BINDING SITE FOR RESIDUE DTP A 803
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: UMUC (A:3-187)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UMUC
PS50173
UmuC domain profile.
DPO4_SULSO
3-187
1
A:3-187
-
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Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1s0ma1 (A:241-341)
1b: SCOP_d1s0mb1 (B:241-341)
2a: SCOP_d1s0ma2 (A:1-240)
2b: SCOP_d1s0mb2 (B:1-240)
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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
d1s0ma1
A:241-341
1b
d1s0mb1
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
d1s0ma2
A:1-240
2b
d1s0mb2
B:1-240
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1s0mA02 (A:2-10,A:78-166)
1b: CATH_1s0mB02 (B:2-10,B:78-166)
2a: CATH_1s0mA04 (A:244-336)
2b: CATH_1s0mB04 (B:244-336)
3a: CATH_1s0mA03 (A:167-233)
3b: CATH_1s0mB03 (B:167-233)
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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)
[unclassified]
(58)
1a
1s0mA02
A:2-10,A:78-166
1b
1s0mB02
B:2-10,B:78-166
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
[code=3.30.1490.100, no name defined]
(80)
[unclassified]
(29)
2a
1s0mA04
A:244-336
2b
1s0mB04
B:244-336
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
[unclassified]
(230)
3a
1s0mA03
A:167-233
3b
1s0mB03
B:167-233
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_IMS_HHH_1s0mB01 (B:168-199)
1b: PFAM_IMS_HHH_1s0mB02 (B:168-199)
2a: PFAM_IMS_1s0mB03 (B:6-156)
2b: PFAM_IMS_1s0mB04 (B:6-156)
3a: PFAM_IMS_C_1s0mB05 (B:211-334)
3b: PFAM_IMS_C_1s0mB06 (B:211-334)
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Organisms
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)
(
)
Clan
:
HHH
(112)
Family
:
IMS_HHH
(56)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(51)
1a
IMS_HHH-1s0mB01
B:168-199
1b
IMS_HHH-1s0mB02
B:168-199
Clan
:
no clan defined [family: IMS]
(76)
Family
:
IMS
(76)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(51)
2a
IMS-1s0mB03
B:6-156
2b
IMS-1s0mB04
B:6-156
Clan
:
no clan defined [family: IMS_C]
(74)
Family
:
IMS_C
(74)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(51)
3a
IMS_C-1s0mB05
B:211-334
3b
IMS_C-1s0mB06
B:211-334
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Asymmetric Unit 1
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Asym.Unit (152 KB)
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