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.
3UBY
Asym. Unit
Info
Asym.Unit (149 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
:
CRYSTAL STRUCTURE OF HUMAN ALKLYADENINE DNA GLYCOSYLASE IN A LOWER AND HIGHER-AFFINITY COMPLEX WITH DNA
Authors
:
J. W. Setser, G. M. Lingaraju, C. A. Davis, L. D. Samson, C. L. Drennan
Date
:
25 Oct 11 (Deposition) - 28 Dec 11 (Release) - 25 Jan 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Alkyladenine Dna Glycosylase Fold, Aag, Dna Repair, Dna Binding, Nucleus, Hydrolase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. W. Setser, G. M. Lingaraju, C. A. Davis, L. D. Samson, C. L. Drennan
Searching For Dna Lesions: Structural Evidence For Lower- And Higher-Affinity Dna Binding Conformations Of Human Alkyladenine Dna Glycosylase.
Biochemistry V. 51 382 2012
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: N3,N4-ETHENO-2'-DEOXYCYTIDINE-5'-M... (EDCa)
1b: N3,N4-ETHENO-2'-DEOXYCYTIDINE-5'-M... (EDCb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDC
2
Mod. Nucleotide
N3,N4-ETHENO-2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
[
close Hetero Component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(4, 7)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_050096 (Q93R, chain A/B, )
2: VAR_014833 (R120C, chain A/B, )
3: VAR_014834 (R141Q, chain A, )
4: VAR_014835 (A258V, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_050096
Q
93
R
3MG_HUMAN
Polymorphism
25671
A/B
Q
93
R
2
UniProt
VAR_014833
R
120
C
3MG_HUMAN
Polymorphism
2308313
A/B
R
120
C
3
UniProt
VAR_014834
R
141
Q
3MG_HUMAN
Polymorphism
2308312
A
R
141
Q
4
UniProt
VAR_014835
A
258
V
3MG_HUMAN
Polymorphism
769193
A/B
A
258
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(3, 6)
Info
All Exons
Exon 1.4a (A:80-105 (gaps) | B:80-105 (gaps))
Exon 1.5 (A:106-174 | B:106-174 (gaps))
Exon 1.6c (A:174-293 (gaps) | B:174-289 (gaps...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.3a/1.4a
2: Boundary 1.4a/1.5
3: Boundary 1.5/1.6c
4: Boundary 1.6c/-
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
1.2d
ENST00000219431
2d
ENSE00001815669
chr16:
128256-128332
77
3MG_HUMAN
-
0
0
-
-
1.3a
ENST00000219431
3a
ENSE00000842196
chr16:
129138-129330
193
3MG_HUMAN
1-13
13
0
-
-
1.4a
ENST00000219431
4a
ENSE00001702894
chr16:
129424-129699
276
3MG_HUMAN
14-105
92
2
A:80-105 (gaps)
B:80-105 (gaps)
37
37
1.5
ENST00000219431
5
ENSE00000663759
chr16:
133051-133255
205
3MG_HUMAN
106-174
69
2
A:106-174
B:106-174 (gaps)
69
69
1.6c
ENST00000219431
6c
ENSE00001892380
chr16:
135400-135841
442
3MG_HUMAN
174-298
125
2
A:174-293 (gaps)
B:174-289 (gaps)
120
116
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3ubya_ (A:)
1b: SCOP_d3ubyb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
FMT C-terminal domain-like
(19)
Superfamily
:
FMT C-terminal domain-like
(19)
Family
:
3-methyladenine DNA glycosylase (AAG, ANPG, MPG)
(6)
Protein domain
:
automated matches
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d3ubya_
A:
1b
d3ubyb_
B:
[
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
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 (149 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
3UBY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help