PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1S0M
Asym. Unit
Info
Asym.Unit (152 KB)
Biol.Unit 1 (75 KB)
Biol.Unit 2 (74 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(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
[
close entry info
]
Hetero Components
(4, 12)
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
2
Ligand/Ion
1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE
2
CA
7
Ligand/Ion
CALCIUM ION
3
DTP
2
Ligand/Ion
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
4
MG
1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:7 , ASP A:105 , GLU A:106 , DTP A:803 , HOH A:917
BINDING SITE FOR RESIDUE MG A 401
02
AC2
SOFTWARE
ASP B:7 , ASP B:105 , GLU B:106 , DTP B:804 , HOH E:171 , DT E:1813
BINDING SITE FOR RESIDUE CA B 403
03
AC3
SOFTWARE
ASP A:7 , PHE A:8 , ASP A:105 , DTP A:803
BINDING SITE FOR RESIDUE CA A 402
04
AC4
SOFTWARE
ASP B:7 , PHE B:8 , ASP B:105 , DTP B:804
BINDING SITE FOR RESIDUE CA B 404
05
AC5
SOFTWARE
ALA B:181 , ILE B:186 , HOH B:851 , HOH B:852 , HOH B:853 , HOH B:889 , HOH E:175 , HOH E:272 , DT E:1812
BINDING SITE FOR RESIDUE CA B 405
06
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
07
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
08
AC8
SOFTWARE
ASP B:294 , HOH B:813 , HOH B:861 , HOH E:122 , DG E:1809
BINDING SITE FOR RESIDUE CA E 408
09
AC9
SOFTWARE
DTP A:803 , HOH C:165 , DT C:1813 , HOH D:33 , DA D:1906
BINDING SITE FOR RESIDUE BAP D 1920
10
BC1
SOFTWARE
ILE B:295 , DTP B:804 , HOH E:167 , DT E:1811 , DT E:1812 , HOH F:311 , DT F:1905 , DA F:1906 , DA F:1907
BINDING SITE FOR RESIDUE BAP F 1920
11
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
12
BC3
SOFTWARE
ASP B:7 , PHE B:8 , ASP B:9 , 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:403 , CA B:404 , HOH B:823 , HOH B:849 , HOH B:868 , DT E:1813 , DT F:1905 , BAP F:1920
BINDING SITE FOR RESIDUE DTP B 804
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: UMUC (A:3-187,B:3-187)
;
View:
Select:
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
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
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_d1s0ma1 (A:241-341)
1b: SCOP_d1s0mb1 (B:241-341)
2a: SCOP_d1s0ma2 (A:1-240)
2b: SCOP_d1s0mb2 (B:1-240)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
[
close SCOP info
]
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)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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
[
close CATH info
]
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)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
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
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (152 KB)
Header - Asym.Unit
Biol.Unit 1 (75 KB)
Header - Biol.Unit 1
Biol.Unit 2 (74 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1S0M
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help