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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2BCQ
Asym. Unit
Info
Asym.Unit (80 KB)
Biol.Unit 1 (74 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
DNA POLYMERASE LAMBDA IN COMPLEX WITH A DNA DUPLEX CONTAINING AN UNPAIRED DTMP
Authors
:
M. Garcia-Diaz, K. Bebenek, J. M. Krahn, L. C. Pedersen, T. A. Kunkel
Date
:
19 Oct 05 (Deposition) - 07 Mar 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,D,P,T
Biol. Unit 1: A,D,P,T (1x)
Keywords
:
Misalignment, Extrahelical, Mutagenesis, Mutation, Deletion, Streisinger, Slippage, Transferase, Lyase/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Garcia-Diaz, K. Bebenek, J. M. Krahn, L. C. Pedersen, T. A. Kunkel
Structural Analysis Of Strand Misalignment During Dna Synthesis By A Human Dna Polymerase
Cell(Cambridge, Mass. ) V. 124 331 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 6)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
2a: MAGNESIUM ION (MGa)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
4a: PYROPHOSPHATE (PPVa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
2
MG
1
Ligand/Ion
MAGNESIUM ION
3
NA
3
Ligand/Ion
SODIUM ION
4
PPV
1
Ligand/Ion
PYROPHOSPHATE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:339 , ILE A:341 , ALA A:344 , HOH A:2815 , DA P:5 , HOH P:37
BINDING SITE FOR RESIDUE NA A 1
2
AC2
SOFTWARE
SER A:463 , HOH A:2833 , HOH A:2875 , HOH A:2927 , HOH A:3042 , HOH T:25
BINDING SITE FOR RESIDUE NA A 4
3
AC3
SOFTWARE
HOH A:2833 , HOH A:3228 , HOH T:55 , HOH T:58 , HOH T:80
BINDING SITE FOR RESIDUE NA A 712
4
AC4
SOFTWARE
ASP A:427 , ASP A:429 , PPV A:738 , DG P:7
BINDING SITE FOR RESIDUE MG A 713
5
AC5
SOFTWARE
ARG A:386 , GLY A:416 , SER A:417 , ARG A:420 , GLY A:426 , ASP A:427 , ASP A:429 , MG A:713 , HOH A:2809 , HOH A:2896 , HOH A:2903 , HOH A:2914 , HOH A:2993 , HOH A:3072 , DG P:7
BINDING SITE FOR RESIDUE PPV A 738
6
AC6
SOFTWARE
GLN A:471 , VAL A:494 , HIS A:530 , HOH A:2813 , HOH A:2844 , HOH A:2850
BINDING SITE FOR RESIDUE EDO A 2801
[
close Site info
]
SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_020269 (R438W, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_020269
R
438
W
DPOLL_HUMAN
Polymorphism
3730477
A
R
438
W
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_X (A:416-435)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_X
PS00522
DNA polymerase family X signature.
DPOLL_HUMAN
416-435
1
A:416-435
[
close PROSITE info
]
Exons
(5, 5)
Info
All Exons
Exon 1.5e (A:252-297)
Exon 1.6b (A:298-355)
Exon 1.7b (A:356-398)
Exon 1.8c (A:399-455)
Exon 1.9g (A:455-575)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.4b/1.5e
2: Boundary 1.5e/1.6b
3: Boundary 1.6b/1.7b
4: Boundary 1.7b/1.8c
5: Boundary 1.8c/1.9g
6: Boundary 1.9g/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1k
ENST00000370169
1k
ENSE00001451987
chr10:
103347178-103347003
176
DPOLL_HUMAN
1-39
39
0
-
-
1.3
ENST00000370169
3
ENSE00001731892
chr10:
103345913-103345619
295
DPOLL_HUMAN
39-137
99
0
-
-
1.4b
ENST00000370169
4b
ENSE00001100422
chr10:
103345235-103345073
163
DPOLL_HUMAN
137-191
55
0
-
-
1.5e
ENST00000370169
5e
ENSE00001617344
chr10:
103344676-103344359
318
DPOLL_HUMAN
192-297
106
1
A:252-297
46
1.6b
ENST00000370169
6b
ENSE00002151653
chr10:
103343438-103343265
174
DPOLL_HUMAN
298-355
58
1
A:298-355
58
1.7b
ENST00000370169
7b
ENSE00001593760
chr10:
103342648-103342520
129
DPOLL_HUMAN
356-398
43
1
A:356-398
43
1.8c
ENST00000370169
8c
ENSE00001691940
chr10:
103340173-103340005
169
DPOLL_HUMAN
399-455
57
1
A:399-455
57
1.9g
ENST00000370169
9g
ENSE00001451993
chr10:
103339574-103338639
936
DPOLL_HUMAN
455-575
121
1
A:455-575
121
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d2bcqa1 (A:252-328)
2a: SCOP_d2bcqa2 (A:329-385)
3a: SCOP_d2bcqa3 (A:386-575)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
SAM domain-like
(639)
Superfamily
:
DNA polymerase beta, N-terminal domain-like
(205)
Family
:
DNA polymerase beta, N-terminal domain-like
(183)
Protein domain
:
DNA polymerase lambda
(24)
Human (Homo sapiens) [TaxId: 9606]
(24)
1a
d2bcqa1
A:252-328
Superfamily
:
PsbU/PolX domain-like
(218)
Family
:
DNA polymerase beta-like, second domain
(190)
Protein domain
:
DNA polymerase lambda
(23)
Human (Homo sapiens) [TaxId: 9606]
(23)
2a
d2bcqa2
A:329-385
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Nucleotidyltransferase
(287)
Superfamily
:
Nucleotidyltransferase
(287)
Family
:
DNA polymerase beta-like
(218)
Protein domain
:
DNA polymerase lambda
(23)
Human (Homo sapiens) [TaxId: 9606]
(23)
3a
d2bcqa3
A:386-575
[
close SCOP info
]
CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_2bcqA03 (A:386-508)
2a: CATH_2bcqA04 (A:509-575)
3a: CATH_2bcqA01 (A:252-331)
4a: CATH_2bcqA02 (A:332-385)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Beta Polymerase; domain 2
(187)
Homologous Superfamily
:
Beta Polymerase, domain 2
(183)
[unclassified]
(117)
1a
2bcqA03
A:386-508
Topology
:
Beta Polymerase; domain 3
(161)
Homologous Superfamily
:
Beta Polymerase, domain 3
(161)
[unclassified]
(116)
2a
2bcqA04
A:509-575
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
[code=1.10.150.110, no name defined]
(150)
[unclassified]
(116)
3a
2bcqA01
A:252-331
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
[unclassified]
(230)
4a
2bcqA02
A:332-385
[
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 D
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 (80 KB)
Header - Asym.Unit
Biol.Unit 1 (74 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
2BCQ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help