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.
1SKR
Asym. Unit
Info
Asym.Unit (148 KB)
Biol.Unit 1 (143 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
T7 DNA POLYMERASE COMPLEXED TO DNA PRIMER/TEMPLATE AND DDATP
Authors
:
Y. Li, S. Dutta, S. Doublie, H. M. Bdour, J. S. Taylor, T. Ellenberger
Date
:
05 Mar 04 (Deposition) - 06 Jul 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,P,T
Biol. Unit 1: A,B,P,T (1x)
Keywords
:
Dna Polymerase, Uv-Lesion, Replication, Open, Close, Transferase/Electron Transport/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Li, S. Dutta, S. Doublie, H. M. Bdour, J. S. Taylor, T. Ellenberger
Nucleotide Insertion Opposite A Cis-Syn Thymine Dimer By A Replicative Dna Polymerase From Bacteriophage T7.
Nat. Struct. Mol. Biol. V. 11 784 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 5)
Info
All Hetero Components
1a: 2',3'-DIDEOXYADENOSINE-5'-MONOPHOS... (2DAa)
2a: 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSP... (DADa)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2DA
1
Mod. Nucleotide
2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE
2
DAD
1
Ligand/Ion
2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE
3
MG
3
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:475 , ALA A:476 , ASP A:654 , DAD A:4004
BINDING SITE FOR RESIDUE MG A 4001
2
AC2
SOFTWARE
ASP A:475 , ASP A:654 , DAD A:4004 , HOH A:5017 , HOH A:5442 , 2DA P:22
BINDING SITE FOR RESIDUE MG A 4002
3
AC3
SOFTWARE
ASP A:5 , HOH A:5031 , HOH A:5044 , HOH A:5432 , HOH A:5433
BINDING SITE FOR RESIDUE MG A 4003
4
AC4
SOFTWARE
ARG A:429 , ASP A:475 , ALA A:476 , SER A:477 , GLY A:478 , LEU A:479 , GLU A:480 , HIS A:506 , ARG A:518 , LYS A:522 , TYR A:526 , ASP A:654 , MG A:4001 , MG A:4002 , HOH A:5008 , HOH A:5055 , HOH A:5168 , HOH A:5251 , HOH A:5284 , 2DA P:22 , DT T:4 , DT T:5
BINDING SITE FOR RESIDUE DAD A 4004
[
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
(2, 2)
Info
All PROSITE Patterns/Profiles
1: THIOREDOXIN_1 (B:24-42)
2: DNA_POLYMERASE_A (A:518-537)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THIOREDOXIN_1
PS00194
Thioredoxin family active site.
THIO_ECOLI
25-43
1
B:24-42
2
DNA_POLYMERASE_A
PS00447
DNA polymerase family A signature.
DPOL_BPT7
518-537
1
A:518-537
[
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
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1skra1 (A:1-210)
2a: SCOP_d1skrb_ (B:)
3a: SCOP_d1skra2 (A:211-704)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Ribonuclease H-like
(775)
Family
:
DnaQ-like 3'-5' exonuclease
(253)
Protein domain
:
Exonuclease domain of T7 DNA polymerase
(17)
Bacteriophage T7 [TaxId: 10760]
(17)
1a
d1skra1
A:1-210
Fold
:
Thioredoxin fold
(994)
Superfamily
:
Thioredoxin-like
(992)
Family
:
Thioltransferase
(167)
Protein domain
:
Thioredoxin
(106)
Escherichia coli [TaxId: 562]
(47)
2a
d1skrb_
B:
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
DNA polymerase I
(233)
Protein domain
:
T7 phage DNA polymerase
(17)
Bacteriophage T7 [TaxId: 10760]
(17)
3a
d1skra2
A:211-704
[
close SCOP info
]
CATH Domains
(5, 5)
Info
all CATH domains
1a: CATH_1skrA03 (A:415-477,A:590-704)
2a: CATH_1skrA01 (A:1-232)
3a: CATH_1skrB00 (B:3-107)
4a: CATH_1skrA04 (A:478-589)
5a: CATH_1skrA02 (A:233-414)
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=3.30.70.370, no name defined]
(99)
[unclassified]
(84)
1a
1skrA03
A:415-477,A:590-704
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.10, no name defined]
(372)
[unclassified]
(102)
2a
1skrA01
A:1-232
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Glutaredoxin
(620)
Homologous Superfamily
:
Glutaredoxin
(617)
[unclassified]
(18)
3a
1skrB00
B:3-107
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)
4a
1skrA04
A:478-589
Architecture
:
Up-down Bundle
(3216)
Topology
:
Taq DNA Polymerase; Chain T, domain 4
(88)
Homologous Superfamily
:
Taq DNA Polymerase; Chain T, domain 4
(88)
[unclassified]
(77)
5a
1skrA02
A:233-414
[
close CATH info
]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_RNase_H_2_1skrA01 (A:2-186)
2a: PFAM_Thioredoxin_1skrB01 (B:3-106)
3a: PFAM_DNA_pol_A_1skrA02 (A:316-703)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
RNase_H
(288)
Family
:
RNase_H_2
(16)
Enterobacteria phage T7 (Bacteriophage T7)
(16)
1a
RNase_H_2-1skrA01
A:2-186
Clan
:
Thioredoxin
(367)
Family
:
Thioredoxin
(82)
Escherichia coli (strain K12)
(25)
2a
Thioredoxin-1skrB01
B:3-106
Clan
:
no clan defined [family: DNA_pol_A]
(69)
Family
:
DNA_pol_A
(69)
Enterobacteria phage T7 (Bacteriophage T7)
(16)
3a
DNA_pol_A-1skrA02
A:316-703
[
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 P
Chain T
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 (148 KB)
Header - Asym.Unit
Biol.Unit 1 (143 KB)
Header - Biol.Unit 1
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
1SKR
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help