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.
2QRV
Biol. Unit 2
Info
Asym.Unit (310 KB)
Biol.Unit 1 (153 KB)
Biol.Unit 2 (152 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF DNMT3A-DNMT3L C-TERMINAL DOMAIN COMPLEX
Authors
:
D. Jia, X. Cheng
Date
:
29 Jul 07 (Deposition) - 04 Dec 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.89
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Dna Methyltransferase 3A (Dnmt3A) And Its Regulatory Factor, Dna Methyltransferase 3-Like Protein (Dnmt3L), Nucleus, S- Adenosyl-L-Methionine, Transferase/Transferase Regulator Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Jia, R. Z. Jurkowska, X. Zhang, A. Jeltsch, X. Cheng
Structure Of Dnmt3A Bound To Dnmt3L Suggests A Model For De Novo Dna Methylation.
Nature V. 449 248 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: S-ADENOSYL-L-HOMOCYSTEINE (SAHa)
1b: S-ADENOSYL-L-HOMOCYSTEINE (SAHb)
1c: S-ADENOSYL-L-HOMOCYSTEINE (SAHc)
1d: S-ADENOSYL-L-HOMOCYSTEINE (SAHd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SAH
2
Ligand/Ion
S-ADENOSYL-L-HOMOCYSTEINE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC3 (SOFTWARE)
2: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
PHE E:636 , GLY E:638 , ILE E:639 , THR E:641 , SER E:659 , GLU E:660 , VAL E:661 , CYS E:662 , ASP E:682 , VAL E:683 , ARG E:684 , GLY E:703 , PRO E:705 , LEU E:726 , ARG E:887 , SER E:888 , TRP E:889
BINDING SITE FOR RESIDUE SAH E 5
2
AC4
SOFTWARE
PHE H:636 , GLY H:638 , ILE H:639 , THR H:641 , GLU H:660 , VAL H:661 , CYS H:662 , ASP H:682 , VAL H:683 , GLY H:703 , ARG H:887 , SER H:888 , TRP H:889
BINDING SITE FOR RESIDUE SAH H 8
[
close Site info
]
SAPs(SNPs)/Variants
(10, 20)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_051962 (R278G, chain F/G, )
02: VAR_071467 (L644P, chain E/H, )
03: VAR_067234 (G695D, chain E/H, )
04: VAR_071468 (P696L, chain E/H, )
05: VAR_071469 (R745C, chain E/H, )
06: VAR_067236 (R878C, chain E/H, )
07: VAR_067237 (R878H, chain E/H, )
08: VAR_067238 (R878P, chain E/H, )
09: VAR_071471 (F898S, chain E/H, )
10: VAR_071472 (P900L, chain E/H, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_051962
R
278
G
DNM3L_HUMAN
Polymorphism
7354779
F/G
R
278
G
02
UniProt
VAR_071467
L
648
P
DNM3A_HUMAN
Disease (TBRS)
---
E/H
L
644
P
03
UniProt
VAR_067234
G
699
D
DNM3A_HUMAN
Unclassified
---
E/H
G
695
D
04
UniProt
VAR_071468
P
700
L
DNM3A_HUMAN
Disease (TBRS)
---
E/H
P
696
L
05
UniProt
VAR_071469
R
749
C
DNM3A_HUMAN
Disease (TBRS)
---
E/H
R
745
C
06
UniProt
VAR_067236
R
882
C
DNM3A_HUMAN
Unclassified
---
E/H
R
878
C
07
UniProt
VAR_067237
R
882
H
DNM3A_HUMAN
Unclassified
---
E/H
R
878
H
08
UniProt
VAR_067238
R
882
P
DNM3A_HUMAN
Unclassified
---
E/H
R
878
P
09
UniProt
VAR_071471
F
902
S
DNM3A_HUMAN
Disease (TBRS)
---
E/H
F
898
S
10
UniProt
VAR_071472
P
904
L
DNM3A_HUMAN
Disease (TBRS)
---
E/H
P
900
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: SAM_MT_C5 (E:630-908,H:630-908)
2: C5_MTASE_1 (E:698-710,H:698-710)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SAM_MT_C5
PS51679
C-5 cytosine-specific DNA methylase (Dnmt) domain profile.
DNM3A_HUMAN
634-912
2
-
-
E:630-908
H:630-908
2
C5_MTASE_1
PS00094
C-5 cytosine-specific DNA methylases active site.
DNM3A_HUMAN
702-714
2
-
-
E:698-710
H:698-710
[
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.
(no "Exon" information available for biological units yet)
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
(1, 4)
Info
all PFAM domains
1a: PFAM_DNA_methylase_2qrvH01 (H:630-772)
1b: PFAM_DNA_methylase_2qrvH02 (H:630-772)
1c: PFAM_DNA_methylase_2qrvH03 (H:630-772)
1d: PFAM_DNA_methylase_2qrvH04 (H:630-772)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
DNA_methylase
(15)
Homo sapiens (Human)
(2)
1a
DNA_methylase-2qrvH01
H:630-772
1b
DNA_methylase-2qrvH02
H:630-772
1c
DNA_methylase-2qrvH03
H:630-772
1d
DNA_methylase-2qrvH04
H:630-772
[
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 E
Chain F
Chain G
Chain H
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 (310 KB)
Header - Asym.Unit
Biol.Unit 1 (153 KB)
Header - Biol.Unit 1
Biol.Unit 2 (152 KB)
Header - Biol.Unit 2
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
2QRV
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help