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.
3RMD
Asym. Unit
Info
Asym.Unit (649 KB)
Biol.Unit 1 (165 KB)
Biol.Unit 2 (170 KB)
Biol.Unit 3 (169 KB)
Biol.Unit 4 (165 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 REPLICATIVE DNA POLYMERASE BOUND TO DNA CONTAINING THYMINE GLYCOL
Authors
:
P. Aller, S. Duclos, S. S. Wallace, S. Doublie
Date
:
20 Apr 11 (Deposition) - 10 Aug 11 (Release) - 02 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.98
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,E,F (1x)
Biol. Unit 2: B,G,H (1x)
Biol. Unit 3: C,I,J (1x)
Biol. Unit 4: D,K,L (1x)
Keywords
:
Dna Lesion, Thymine Glycol, Protein-Dna Complex, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Aller, S. Duclos, S. S. Wallace, S. Doublie
A Crystallographic Study Of The Role Of Sequence Context In Thymine Glycol Bypass By A Replicative Dna Polymerase Serendipitously Sheds Light On The Exonuclease Complex.
J. Mol. Biol. V. 412 22 2011
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 5)
Info
All Hetero Components
1a: (5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYT... (CTGa)
1b: (5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYT... (CTGb)
1c: (5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYT... (CTGc)
2a: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPa)
2b: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CTG
3
Mod. Nucleotide
(5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5'-MONOPHOSPHATE
2
DTP
2
Ligand/Ion
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER B:414 , LEU B:415 , TYR B:416 , ARG B:482 , LYS B:560 , ASP B:623 , DT G:3 , DA H:115
BINDING SITE FOR RESIDUE DTP B 907
2
AC2
SOFTWARE
TYR C:416 , ASN C:564 , DT I:3 , DA J:115
BINDING SITE FOR RESIDUE DTP J 2
[
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, 4)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_B (A:619-627,B:619-627,C:619-627,D:61...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_B
PS00116
DNA polymerase family B signature.
DPOL_BPR69
619-627
4
A:619-627
B:619-627
C:619-627
D:619-627
[
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, 8)
Info
All SCOP Domains
1a: SCOP_d3rmda1 (A:1-375)
1b: SCOP_d3rmdb1 (B:1-375)
1c: SCOP_d3rmdc1 (C:1-375)
1d: SCOP_d3rmdd1 (D:1-375)
2a: SCOP_d3rmda2 (A:376-902)
2b: SCOP_d3rmdb2 (B:376-902)
2c: SCOP_d3rmdc2 (C:376-901)
2d: SCOP_d3rmdd2 (D:376-897)
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 family B DNA polymerases
(102)
Bacteriophage RB69 [TaxId: 12353]
(92)
1a
d3rmda1
A:1-375
1b
d3rmdb1
B:1-375
1c
d3rmdc1
C:1-375
1d
d3rmdd1
D:1-375
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
:
Family B DNA polymerase
(100)
Bacteriophage RB69 [TaxId: 12353]
(92)
2a
d3rmda2
A:376-902
2b
d3rmdb2
B:376-902
2c
d3rmdc2
C:376-901
2d
d3rmdd2
D:376-897
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
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 (649 KB)
Header - Asym.Unit
Biol.Unit 1 (165 KB)
Header - Biol.Unit 1
Biol.Unit 2 (170 KB)
Header - Biol.Unit 2
Biol.Unit 3 (169 KB)
Header - Biol.Unit 3
Biol.Unit 4 (165 KB)
Header - Biol.Unit 4
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
3RMD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
