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.
3CQ8
Asym. Unit
Info
Asym.Unit (179 KB)
Biol.Unit 1 (172 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
TERNARY COMPLEX OF THE L415F MUTANT RB69 EXO(-)POLYMERASE
Authors
:
X. Zhong, L. C. Pedersen, T. A. Kunkel
Date
:
02 Apr 08 (Deposition) - 02 Sep 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,P,T
Biol. Unit 1: A,P,T (1x)
Keywords
:
B Family Polymerase Fold, Dna Replication, Dna-Binding, Dna-Directed Dna Polymerase, Exonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Zhong, L. C. Pedersen, T. A. Kunkel
Characterization Of A Replicative Dna Polymerase Mutant Wit Reduced Fidelity And Increased Translesion Synthesis Capacity.
Nucleic Acids Res. V. 36 3892 2008
[
close entry info
]
Hetero Components
(4, 13)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
4a: THYMIDINE-5'-TRIPHOSPHATE (TTPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
6
Ligand/Ion
CALCIUM ION
2
GOL
3
Ligand/Ion
GLYCEROL
3
NA
3
Ligand/Ion
SODIUM ION
4
TTP
1
Ligand/Ion
THYMIDINE-5'-TRIPHOSPHATE
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:411 , LEU A:412 , ASP A:623
BINDING SITE FOR RESIDUE CA A 1001
02
AC2
SOFTWARE
ASP A:411 , ASP A:623
BINDING SITE FOR RESIDUE CA A 1002
03
AC3
SOFTWARE
GLU A:686 , GLU A:716 , HOH A:1298 , HOH A:1300 , HOH A:1484
BINDING SITE FOR RESIDUE CA A 1003
04
AC4
SOFTWARE
CYS A:671 , HOH A:1360
BINDING SITE FOR RESIDUE CA A 1004
05
AC5
SOFTWARE
ASP A:114 , ILE A:115 , GLU A:116 , HOH A:1387 , HOH A:1401 , HOH A:1435
BINDING SITE FOR RESIDUE CA A 1005
06
AC6
SOFTWARE
GLU A:660 , ASP A:684 , HOH A:1310
BINDING SITE FOR RESIDUE CA A 1006
07
AC7
SOFTWARE
GLU A:172 , GLU A:177
BINDING SITE FOR RESIDUE NA A 1007
08
AC8
SOFTWARE
ASN A:505 , ASN A:507 , LYS A:531
BINDING SITE FOR RESIDUE NA A 1008
09
AC9
SOFTWARE
ASN A:606 , GLY A:610 , THR A:611 , GLU A:612
BINDING SITE FOR RESIDUE NA A 1009
10
BC1
SOFTWARE
ASP A:411 , LEU A:412 , THR A:413 , SER A:414 , PHE A:415 , TYR A:416 , ARG A:482 , LYS A:560 , ASN A:564 , ASP A:623 , HOH A:1114 , HOH A:1476 , DC P:115 , DA T:3 , DG T:4
BINDING SITE FOR RESIDUE TTP A 1010
11
BC2
SOFTWARE
HIS A:105 , ASN A:342 , HOH A:1306 , HOH A:1308
BINDING SITE FOR RESIDUE GOL A 1100
12
BC3
SOFTWARE
GLU A:181 , LYS A:185 , TYR A:329 , HOH A:1303 , HOH A:1426
BINDING SITE FOR RESIDUE GOL A 1101
13
BC4
SOFTWARE
ARG A:384 , TYR A:578 , ASP A:579
BINDING SITE FOR RESIDUE GOL A 1102
[
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, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_B (A:619-627)
;
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
1
A: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, 2)
Info
All SCOP Domains
1a: SCOP_d3cq8a1 (A:1-375)
2a: SCOP_d3cq8a2 (A:376-902)
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
d3cq8a1
A: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
d3cq8a2
A:376-902
[
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 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 (179 KB)
Header - Asym.Unit
Biol.Unit 1 (172 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
3CQ8
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
