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3A1A
Asym. Unit
Info
Asym.Unit (31 KB)
Biol.Unit 1 (22 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE DNMT3A ADD DOMAIN
Authors
:
J. Otani, K. Arita, M. Ariyoshi, M. Shirakawa
Date
:
28 Mar 09 (Deposition) - 10 Nov 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Zinc-Finger, Alternative Promoter Usage, Dna-Binding, Metal-Binding, Methyltransferase, Nucleus, Phosphoprotein, S-Adenosyl-L-Methionine, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Otani, T. Nankumo, K. Arita, S. Inamoto, M. Ariyoshi, M. Shirakawa
Structural Basis For Recognition Of H3K4 Methylation Status By The Dna Methyltransferase 3A Atrx-Dnmt3-Dnmt3L Domain
Embo Rep. V. 10 1235 2009
[
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
2
ZN
3
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:494 , CYS A:497 , CYS A:514 , CYS A:517
BINDING SITE FOR RESIDUE ZN A 1
2
AC2
SOFTWARE
CYS A:537 , CYS A:540 , CYS A:559 , CYS A:562
BINDING SITE FOR RESIDUE ZN A 2
3
AC3
SOFTWARE
CYS A:549 , CYS A:554 , CYS A:583 , CYS A:586
BINDING SITE FOR RESIDUE ZN A 3
4
AC4
SOFTWARE
HOH A:14 , PHE A:521 , CYS A:524 , ALA A:525 , TYR A:536 , CYS A:537 , CYS A:541
BINDING SITE FOR RESIDUE EDO A 4
[
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]
SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_071464 (G532S, chain A, )
2: VAR_071465 (M548K, chain A, )
3: VAR_071466 (C549R, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_071464
G
532
S
DNM3A_HUMAN
Disease (TBRS)
---
A
G
532
S
2
UniProt
VAR_071465
M
548
K
DNM3A_HUMAN
Disease (TBRS)
---
A
M
548
K
3
UniProt
VAR_071466
C
549
R
DNM3A_HUMAN
Disease (TBRS)
---
A
C
549
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: ADD (A:482-609)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADD
PS51533
ADD domain profile.
DNM3A_HUMAN
482-614
1
A:482-609
[
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]
Exons
(5, 5)
Info
All Exons
Exon 1.15a (A:474-477)
Exon 1.16 (A:477-492)
Exon 1.17b (A:492-518)
Exon 1.18 (A:519-556)
Exon 1.19b (A:556-609 (gaps))
View:
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Label:
All Exon Boundaries
1: Boundary 1.14c/1.15a
2: Boundary 1.15a/1.16
3: Boundary 1.16/1.17b
4: Boundary 1.17b/1.18
5: Boundary 1.18/1.19b
6: Boundary 1.19b/1.20a
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
1.2
ENST00000321117
2
ENSE00001522911
chr2:
25564754-25564695
60
DNM3A_HUMAN
-
0
0
-
-
1.3
ENST00000321117
3
ENSE00001408175
chr2:
25537030-25536782
249
DNM3A_HUMAN
1-24
24
0
-
-
1.4
ENST00000321117
4
ENSE00000808934
chr2:
25523112-25523008
105
DNM3A_HUMAN
25-59
35
0
-
-
1.5a
ENST00000321117
5a
ENSE00001326003
chr2:
25505580-25505310
271
DNM3A_HUMAN
60-150
91
0
-
-
1.6
ENST00000321117
6
ENSE00001486208
chr2:
25498412-25498369
44
DNM3A_HUMAN
150-164
15
0
-
-
1.7
ENST00000321117
7
ENSE00000808931
chr2:
25497956-25497810
147
DNM3A_HUMAN
165-213
49
0
-
-
1.11
ENST00000321117
11
ENSE00001739049
chr2:
25471121-25470906
216
DNM3A_HUMAN
214-285
72
0
-
-
1.12b
ENST00000321117
12b
ENSE00001281470
chr2:
25470618-25470460
159
DNM3A_HUMAN
286-338
53
0
-
-
1.13b
ENST00000321117
13b
ENSE00001071033
chr2:
25470027-25469920
108
DNM3A_HUMAN
339-374
36
0
-
-
1.14c
ENST00000321117
14c
ENSE00001281455
chr2:
25469645-25469489
157
DNM3A_HUMAN
375-427
53
0
-
-
1.15a
ENST00000321117
15a
ENSE00001071035
chr2:
25469178-25469029
150
DNM3A_HUMAN
427-477
51
1
A:474-477
4
1.16
ENST00000321117
16
ENSE00001281442
chr2:
25468933-25468889
45
DNM3A_HUMAN
477-492
16
1
A:477-492
16
1.17b
ENST00000321117
17b
ENSE00001071029
chr2:
25468201-25468122
80
DNM3A_HUMAN
492-518
27
1
A:492-518
27
1.18
ENST00000321117
18
ENSE00001071031
chr2:
25467521-25467409
113
DNM3A_HUMAN
519-556
38
1
A:519-556
38
1.19b
ENST00000321117
19b
ENSE00001281418
chr2:
25467207-25467024
184
DNM3A_HUMAN
556-617
62
1
A:556-609 (gaps)
54
1.20a
ENST00000321117
20a
ENSE00001281558
chr2:
25466851-25466767
85
DNM3A_HUMAN
618-646
29
0
-
-
1.21c
ENST00000321117
21c
ENSE00001071020
chr2:
25464576-25464431
146
DNM3A_HUMAN
646-694
49
0
-
-
1.22
ENST00000321117
22
ENSE00001071021
chr2:
25463599-25463509
91
DNM3A_HUMAN
695-725
31
0
-
-
1.23
ENST00000321117
23
ENSE00001726066
chr2:
25463319-25463171
149
DNM3A_HUMAN
725-774
50
0
-
-
1.25b
ENST00000321117
25b
ENSE00001622127
chr2:
25462084-25461999
86
DNM3A_HUMAN
775-803
29
0
-
-
1.26b
ENST00000321117
26b
ENSE00001679782
chr2:
25459874-25459805
70
DNM3A_HUMAN
803-826
24
0
-
-
1.27b
ENST00000321117
27b
ENSE00001765738
chr2:
25458694-25458576
119
DNM3A_HUMAN
827-866
40
0
-
-
1.28c
ENST00000321117
28c
ENSE00001761921
chr2:
25457289-25455845
1445
DNM3A_HUMAN
866-912
47
0
-
-
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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Chain A
Asymmetric Unit 1
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