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.
3PY8
Asym. Unit
Info
Asym.Unit (211 KB)
Biol.Unit 1 (201 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 MUTANT OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS IN A CLOSED TERNARY COMPLEX WITH DNA AND DDCTP
Authors
:
A. Schnur, A. Marx, W. Welte, K. Diederichs
Date
:
12 Dec 10 (Deposition) - 15 Jun 11 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.74
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Modified Klenow Fragment, Transferase, Polymerase, Nucleoside Binding, Nucleic Acid Binding, Dna Binding, Catalytic Activity, Dna- Directed Dna Polymerase Activity, 5'-3' Exonuclease Activity, Nucleotides, Modified Nucleotide, Artificial Nucleotide, Nucleotide Probes, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Obeid, A. Schnur, C. Gloeckner, N. Blatter, W. Welte, K. Diederichs A. Marx
Learning From Directed Evolution: Thermus Aquaticus Dna Polymerase Mutants With Translesion Synthesis Activity.
Chembiochem V. 12 1574 2011
[
close entry info
]
Hetero Components
(5, 10)
Info
All Hetero Components
1a: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPH... (DCTa)
2a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
4a: MAGNESIUM ION (MGa)
5a: MANGANESE (II) ION (MNa)
5b: MANGANESE (II) ION (MNb)
5c: MANGANESE (II) ION (MNc)
5d: MANGANESE (II) ION (MNd)
5e: MANGANESE (II) ION (MNe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DCT
1
Ligand/Ion
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
2
DOC
1
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3
GOL
2
Ligand/Ion
GLYCEROL
4
MG
1
Ligand/Ion
MAGNESIUM ION
5
MN
5
Ligand/Ion
MANGANESE (II) ION
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
MG A:2 , HOH A:65 , HOH A:100 , HOH A:205 , HOH A:212 , ARG A:573 , ASP A:610 , TYR A:611 , SER A:612 , GLN A:613 , LYS A:614 , GLU A:615 , HIS A:639 , ARG A:659 , LYS A:663 , PHE A:667 , ASP A:785 , MN A:833 , HOH A:858 , HOH A:956 , HOH A:983 , HOH B:29 , DOC B:112 , DG C:204 , DG C:205
BINDING SITE FOR RESIDUE DCT A 113
2
AC2
SOFTWARE
HOH A:176 , HOH A:211 , THR A:544 , TYR A:545 , PRO A:579 , ASN A:580 , ASN A:583 , DC C:209 , DC C:210
BINDING SITE FOR RESIDUE GOL A 1
3
AC3
SOFTWARE
MG A:2 , DCT A:113 , ASP A:610 , TYR A:611 , ASP A:785
BINDING SITE FOR RESIDUE MN A 833
4
AC4
SOFTWARE
DCT A:113 , HOH A:205 , ASP A:610 , ASP A:785 , MN A:833 , HOH A:870 , DOC B:112
BINDING SITE FOR RESIDUE MG A 2
5
AC5
SOFTWARE
HOH A:157 , HOH A:213 , GLU A:462 , GLU A:465 , GLU A:602 , HOH A:904
BINDING SITE FOR RESIDUE MN A 5
6
AC6
SOFTWARE
HOH A:263 , HOH A:274 , HOH A:278 , HIS A:443 , HOH A:941
BINDING SITE FOR RESIDUE MN A 6
7
AC7
SOFTWARE
GLU A:432
BINDING SITE FOR RESIDUE GOL A 834
8
AC8
SOFTWARE
DG B:107 , HOH B:220 , HOH B:312 , HOH B:342 , HOH B:410 , HOH B:469
BINDING SITE FOR RESIDUE MN B 3
9
AC9
SOFTWARE
HOH C:185 , HOH C:186 , DG C:205 , HOH C:218 , HOH C:240 , HOH C:250
BINDING SITE FOR RESIDUE MN C 4
[
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_A (A:659-678)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_A
PS00447
DNA polymerase family A signature.
DPO1_THEAQ
659-678
1
A:659-678
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_DNA_pol_A_3py8A01 (A:451-830)
2a: PFAM_Taq_exonuc_3py8A02 (A:294-420)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: DNA_pol_A]
(69)
Family
:
DNA_pol_A
(69)
Thermus aquaticus
(17)
1a
DNA_pol_A-3py8A01
A:451-830
Clan
:
no clan defined [family: Taq-exonuc]
(17)
Family
:
Taq-exonuc
(17)
Thermus aquaticus
(17)
2a
Taq-exonuc-3py8A02
A:294-420
[
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
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 (211 KB)
Header - Asym.Unit
Biol.Unit 1 (201 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
3PY8
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help