0.024063
0.000000
0.000114
0.000000
0.017723
0.000000
0.000000
0.000000
0.017452
0.00000
0.00000
0.00000
Li, H.
Patel, D.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.27
90.00
41.557
56.424
57.301
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
Zn 2
65.409
ZINC ION
non-polymer
To be Published
0353
Engineering of a histone-recognition domain in a de novo DNA methyltransferase alters the epigenetic landscape of ESCs
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2010-06-30
ADSC QUANTUM 315
Si 111 CHANNEL
SINGLE WAVELENGTH
M
x-ray
1
0.9792
1.0
24-ID-E
APS
0.9792
SYNCHROTRON
APS BEAMLINE 24-ID-E
15386.763
DNA (cytosine-5)-methyltransferase 3A
2.1.1.37
ADD Domain, UNP residues 476-611
2
man
polymer
934.075
Histone H3
H3 N-terminal 1-15
1
syn
polymer
65.409
ZINC ION
6
syn
non-polymer
18.015
water
104
nat
water
Dnmt3a, DNA methyltransferase HsaIIIA, DNA MTase HsaIIIA, M.HsaIIIA
no
no
GPLGSLVYEVRQKCRNIEDICISCGSLNVTLEHPLFVGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNN
CCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRREDWPSRLQMFFA
GPLGSLVYEVRQKCRNIEDICISCGSLNVTLEHPLFVGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNN
CCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRREDWPSRLQMFFA
A,C
polypeptide(L)
no
no
ARTKQTAR
ARTKQTAR
P
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
sample
DNMT3A
9606
Homo sapiens
562
Escherichia coli
1
2.12
41.95
VAPOR DIFFUSION, HANGING DROP
6.5
29% PEGMME5000, 0.1M Bis-Tris Propane-HCL, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
repository
Initial release
1
0
2015-05-13
RCSB
Y
PDBJ
2014-05-08
REL
REL
ZN
ZINC ION
HOH
water
This sequence occurs naturally in humans.
9606
Homo sapiens
sample
THE SEQUENCE OF THE ENTITY2 OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. AUTHORS STATE THAT THE ENTITY2 HAS THE GENEBANK ACCESSION NUMBER AAH43617.1.
ZN2
1
3
ZN
ZN
701
A
ZN2
2
3
ZN
ZN
702
A
ZN2
3
3
ZN
ZN
703
A
ZN2
1
3
ZN
ZN
701
C
ZN2
2
3
ZN
ZN
702
C
ZN2
3
3
ZN
ZN
703
C
HOH
1
4
HOH
HOH
801
A
HOH
2
4
HOH
HOH
802
A
HOH
4
4
HOH
HOH
803
A
HOH
7
4
HOH
HOH
804
A
HOH
8
4
HOH
HOH
805
A
HOH
10
4
HOH
HOH
806
A
HOH
11
4
HOH
HOH
807
A
HOH
12
4
HOH
HOH
808
A
HOH
13
4
HOH
HOH
809
A
HOH
14
4
HOH
HOH
810
A
HOH
15
4
HOH
HOH
811
A
HOH
16
4
HOH
HOH
812
A
HOH
17
4
HOH
HOH
813
A
HOH
19
4
HOH
HOH
814
A
HOH
21
4
HOH
HOH
815
A
HOH
23
4
HOH
HOH
816
A
HOH
24
4
HOH
HOH
817
A
HOH
25
4
HOH
HOH
818
A
HOH
26
4
HOH
HOH
819
A
HOH
28
4
HOH
HOH
820
A
HOH
30
4
HOH
HOH
821
A
HOH
31
4
HOH
HOH
822
A
HOH
37
4
HOH
HOH
823
A
HOH
40
4
HOH
HOH
824
A
HOH
41
4
HOH
HOH
825
A
HOH
43
4
HOH
HOH
826
A
HOH
44
4
HOH
HOH
827
A
HOH
45
4
HOH
HOH
828
A
HOH
49
4
HOH
HOH
829
A
HOH
53
4
HOH
HOH
830
A
HOH
58
4
HOH
HOH
831
A
HOH
60
4
HOH
HOH
832
A
HOH
69
4
HOH
HOH
833
A
HOH
71
4
HOH
HOH
834
A
HOH
73
4
HOH
HOH
835
A
HOH
74
4
HOH
HOH
836
A
HOH
75
4
HOH
HOH
837
A
HOH
76
4
HOH
HOH
838
A
HOH
79
4
HOH
HOH
839
A
HOH
80
4
HOH
HOH
840
A
HOH
82
4
HOH
HOH
841
A
HOH
83
4
HOH
HOH
842
A
HOH
85
4
HOH
HOH
843
A
HOH
87
4
HOH
HOH
844
A
HOH
88
4
HOH
HOH
845
A
HOH
90
4
HOH
HOH
846
A
HOH
91
4
HOH
HOH
847
A
HOH
93
4
HOH
HOH
848
A
HOH
94
4
HOH
HOH
849
A
HOH
95
4
HOH
HOH
850
A
HOH
97
4
HOH
HOH
851
A
HOH
98
4
HOH
HOH
852
A
HOH
100
4
HOH
HOH
853
A
HOH
3
4
HOH
HOH
801
C
HOH
5
4
HOH
HOH
802
C
HOH
6
4
HOH
HOH
803
C
HOH
9
4
HOH
HOH
804
C
HOH
18
4
HOH
HOH
805
C
HOH
20
4
HOH
HOH
806
C
HOH
22
4
HOH
HOH
807
C
HOH
27
4
HOH
HOH
808
C
HOH
29
4
HOH
HOH
809
C
HOH
32
4
HOH
HOH
810
C
HOH
33
4
HOH
HOH
811
C
HOH
34
4
HOH
HOH
812
C
HOH
35
4
HOH
HOH
813
C
HOH
36
4
HOH
HOH
814
C
HOH
38
4
HOH
HOH
815
C
HOH
39
4
HOH
HOH
816
C
HOH
42
4
HOH
HOH
817
C
HOH
46
4
HOH
HOH
818
C
HOH
47
4
HOH
HOH
819
C
HOH
48
4
HOH
HOH
820
C
HOH
51
4
HOH
HOH
821
C
HOH
52
4
HOH
HOH
822
C
HOH
54
4
HOH
HOH
823
C
HOH
55
4
HOH
HOH
824
C
HOH
56
4
HOH
HOH
825
C
HOH
57
4
HOH
HOH
826
C
HOH
61
4
HOH
HOH
827
C
HOH
62
4
HOH
HOH
828
C
HOH
63
4
HOH
HOH
829
C
HOH
64
4
HOH
HOH
830
C
HOH
65
4
HOH
HOH
831
C
HOH
66
4
HOH
HOH
832
C
HOH
67
4
HOH
HOH
833
C
HOH
68
4
HOH
HOH
834
C
HOH
70
4
HOH
HOH
835
C
HOH
72
4
HOH
HOH
836
C
HOH
77
4
HOH
HOH
837
C
HOH
78
4
HOH
HOH
838
C
HOH
81
4
HOH
HOH
839
C
HOH
84
4
HOH
HOH
840
C
HOH
86
4
HOH
HOH
841
C
HOH
89
4
HOH
HOH
842
C
HOH
92
4
HOH
HOH
843
C
HOH
96
4
HOH
HOH
844
C
HOH
99
4
HOH
HOH
845
C
HOH
101
4
HOH
HOH
846
C
HOH
102
4
HOH
HOH
847
C
HOH
103
4
HOH
HOH
848
C
HOH
104
4
HOH
HOH
849
C
HOH
50
4
HOH
HOH
101
P
HOH
59
4
HOH
HOH
102
P
GLY
474
n
1
GLY
474
A
PRO
475
n
2
PRO
475
A
LEU
476
n
3
LEU
476
A
GLY
477
n
4
GLY
477
A
SER
478
n
5
SER
478
A
LEU
479
n
6
LEU
479
A
VAL
480
n
7
VAL
480
A
TYR
481
n
8
TYR
481
A
GLU
482
n
9
GLU
482
A
VAL
483
n
10
VAL
483
A
ARG
484
n
11
ARG
484
A
GLN
485
n
12
GLN
485
A
LYS
486
n
13
LYS
486
A
CYS
487
n
14
CYS
487
A
ARG
488
n
15
ARG
488
A
ASN
489
n
16
ASN
489
A
ILE
490
n
17
ILE
490
A
GLU
491
n
18
GLU
491
A
ASP
492
n
19
ASP
492
A
ILE
493
n
20
ILE
493
A
CYS
494
n
21
CYS
494
A
ILE
495
n
22
ILE
495
A
SER
496
n
23
SER
496
A
CYS
497
n
24
CYS
497
A
GLY
498
n
25
GLY
498
A
SER
499
n
26
SER
499
A
LEU
500
n
27
LEU
500
A
ASN
501
n
28
ASN
501
A
VAL
502
n
29
VAL
502
A
THR
503
n
30
THR
503
A
LEU
504
n
31
LEU
504
A
GLU
505
n
32
GLU
505
A
HIS
506
n
33
HIS
506
A
PRO
507
n
34
PRO
507
A
LEU
508
n
35
LEU
508
A
PHE
509
n
36
PHE
509
A
VAL
510
n
37
VAL
510
A
GLY
511
n
38
GLY
511
A
GLY
512
n
39
GLY
512
A
MET
513
n
40
MET
513
A
CYS
514
n
41
CYS
514
A
GLN
515
n
42
GLN
515
A
ASN
516
n
43
ASN
516
A
CYS
517
n
44
CYS
517
A
LYS
518
n
45
LYS
518
A
ASN
519
n
46
ASN
519
A
CYS
520
n
47
CYS
520
A
PHE
521
n
48
PHE
521
A
LEU
522
n
49
LEU
522
A
GLU
523
n
50
GLU
523
A
CYS
524
n
51
CYS
524
A
ALA
525
n
52
ALA
525
A
TYR
526
n
53
TYR
526
A
GLN
527
n
54
GLN
527
A
TYR
528
n
55
TYR
528
A
ASP
529
n
56
ASP
529
A
ASP
530
n
57
ASP
530
A
ASP
531
n
58
ASP
531
A
GLY
532
n
59
GLY
532
A
TYR
533
n
60
TYR
533
A
GLN
534
n
61
GLN
534
A
SER
535
n
62
SER
535
A
TYR
536
n
63
TYR
536
A
CYS
537
n
64
CYS
537
A
THR
538
n
65
THR
538
A
ILE
539
n
66
ILE
539
A
CYS
540
n
67
CYS
540
A
CYS
541
n
68
CYS
541
A
GLY
542
n
69
GLY
542
A
GLY
543
n
70
GLY
543
A
ARG
544
n
71
ARG
544
A
GLU
545
n
72
GLU
545
A
VAL
546
n
73
VAL
546
A
LEU
547
n
74
LEU
547
A
MET
548
n
75
MET
548
A
CYS
549
n
76
CYS
549
A
GLY
550
n
77
GLY
550
A
ASN
551
n
78
ASN
551
A
ASN
552
n
79
ASN
552
A
ASN
553
n
80
ASN
553
A
CYS
554
n
81
CYS
554
A
CYS
555
n
82
CYS
555
A
ARG
556
n
83
ARG
556
A
CYS
557
n
84
CYS
557
A
PHE
558
n
85
PHE
558
A
CYS
559
n
86
CYS
559
A
VAL
560
n
87
VAL
560
A
GLU
561
n
88
GLU
561
A
CYS
562
n
89
CYS
562
A
VAL
563
n
90
VAL
563
A
ASP
564
n
91
ASP
564
A
LEU
565
n
92
LEU
565
A
LEU
566
n
93
LEU
566
A
VAL
567
n
94
VAL
567
A
GLY
568
n
95
GLY
568
A
PRO
569
n
96
PRO
569
A
GLY
570
n
97
GLY
570
A
ALA
571
n
98
ALA
571
A
ALA
572
n
99
ALA
572
A
GLN
573
n
100
GLN
573
A
ALA
574
n
101
ALA
574
A
ALA
575
n
102
ALA
575
A
ILE
576
n
103
ILE
576
A
LYS
577
n
104
LYS
577
A
GLU
578
n
105
GLU
578
A
ASP
579
n
106
ASP
579
A
PRO
580
n
107
PRO
580
A
TRP
581
n
108
TRP
581
A
ASN
582
n
109
ASN
582
A
CYS
583
n
110
CYS
583
A
TYR
584
n
111
TYR
584
A
MET
585
n
112
MET
585
A
CYS
586
n
113
CYS
586
A
GLY
587
n
114
GLY
587
A
HIS
588
n
115
HIS
588
A
LYS
589
n
116
LYS
589
A
GLY
590
n
117
GLY
590
A
THR
591
n
118
THR
591
A
TYR
592
n
119
TYR
592
A
GLY
593
n
120
GLY
593
A
LEU
594
n
121
LEU
594
A
LEU
595
n
122
LEU
595
A
ARG
596
n
123
ARG
596
A
ARG
597
n
124
ARG
597
A
ARG
598
n
125
ARG
598
A
GLU
599
n
126
GLU
599
A
ASP
600
n
127
ASP
600
A
TRP
601
n
128
TRP
601
A
PRO
602
n
129
PRO
602
A
SER
603
n
130
SER
603
A
ARG
604
n
131
ARG
604
A
LEU
605
n
132
LEU
605
A
GLN
606
n
133
GLN
606
A
MET
607
n
134
MET
607
A
PHE
608
n
135
PHE
608
A
PHE
609
n
136
PHE
609
A
ALA
610
n
137
ALA
610
A
GLY
474
n
1
GLY
474
C
PRO
475
n
2
PRO
475
C
LEU
476
n
3
LEU
476
C
GLY
477
n
4
GLY
477
C
SER
478
n
5
SER
478
C
LEU
479
n
6
LEU
479
C
VAL
480
n
7
VAL
480
C
TYR
481
n
8
TYR
481
C
GLU
482
n
9
GLU
482
C
VAL
483
n
10
VAL
483
C
ARG
484
n
11
ARG
484
C
GLN
485
n
12
GLN
485
C
LYS
486
n
13
LYS
486
C
CYS
487
n
14
CYS
487
C
ARG
488
n
15
ARG
488
C
ASN
489
n
16
ASN
489
C
ILE
490
n
17
ILE
490
C
GLU
491
n
18
GLU
491
C
ASP
492
n
19
ASP
492
C
ILE
493
n
20
ILE
493
C
CYS
494
n
21
CYS
494
C
ILE
495
n
22
ILE
495
C
SER
496
n
23
SER
496
C
CYS
497
n
24
CYS
497
C
GLY
498
n
25
GLY
498
C
SER
499
n
26
SER
499
C
LEU
500
n
27
LEU
500
C
ASN
501
n
28
ASN
501
C
VAL
502
n
29
VAL
502
C
THR
503
n
30
THR
503
C
LEU
504
n
31
LEU
504
C
GLU
505
n
32
GLU
505
C
HIS
506
n
33
HIS
506
C
PRO
507
n
34
PRO
507
C
LEU
508
n
35
LEU
508
C
PHE
509
n
36
PHE
509
C
VAL
510
n
37
VAL
510
C
GLY
511
n
38
GLY
511
C
GLY
512
n
39
GLY
512
C
MET
513
n
40
MET
513
C
CYS
514
n
41
CYS
514
C
GLN
515
n
42
GLN
515
C
ASN
516
n
43
ASN
516
C
CYS
517
n
44
CYS
517
C
LYS
518
n
45
LYS
518
C
ASN
519
n
46
ASN
519
C
CYS
520
n
47
CYS
520
C
PHE
521
n
48
PHE
521
C
LEU
522
n
49
LEU
522
C
GLU
523
n
50
GLU
523
C
CYS
524
n
51
CYS
524
C
ALA
525
n
52
ALA
525
C
TYR
526
n
53
TYR
526
C
GLN
527
n
54
GLN
527
C
TYR
528
n
55
TYR
528
C
ASP
529
n
56
ASP
529
C
ASP
530
n
57
ASP
530
C
ASP
531
n
58
ASP
531
C
GLY
532
n
59
GLY
532
C
TYR
533
n
60
TYR
533
C
GLN
534
n
61
GLN
534
C
SER
535
n
62
SER
535
C
TYR
536
n
63
TYR
536
C
CYS
537
n
64
CYS
537
C
THR
538
n
65
THR
538
C
ILE
539
n
66
ILE
539
C
CYS
540
n
67
CYS
540
C
CYS
541
n
68
CYS
541
C
GLY
542
n
69
GLY
542
C
GLY
543
n
70
GLY
543
C
ARG
544
n
71
ARG
544
C
GLU
545
n
72
GLU
545
C
VAL
546
n
73
VAL
546
C
LEU
547
n
74
LEU
547
C
MET
548
n
75
MET
548
C
CYS
549
n
76
CYS
549
C
GLY
550
n
77
GLY
550
C
ASN
551
n
78
ASN
551
C
ASN
552
n
79
ASN
552
C
ASN
553
n
80
ASN
553
C
CYS
554
n
81
CYS
554
C
CYS
555
n
82
CYS
555
C
ARG
556
n
83
ARG
556
C
CYS
557
n
84
CYS
557
C
PHE
558
n
85
PHE
558
C
CYS
559
n
86
CYS
559
C
VAL
560
n
87
VAL
560
C
GLU
561
n
88
GLU
561
C
CYS
562
n
89
CYS
562
C
VAL
563
n
90
VAL
563
C
ASP
564
n
91
ASP
564
C
LEU
565
n
92
LEU
565
C
LEU
566
n
93
LEU
566
C
VAL
567
n
94
VAL
567
C
GLY
568
n
95
GLY
568
C
PRO
569
n
96
PRO
569
C
GLY
570
n
97
GLY
570
C
ALA
571
n
98
ALA
571
C
ALA
572
n
99
ALA
572
C
GLN
573
n
100
GLN
573
C
ALA
574
n
101
ALA
574
C
ALA
575
n
102
ALA
575
C
ILE
576
n
103
ILE
576
C
LYS
577
n
104
LYS
577
C
GLU
578
n
105
GLU
578
C
ASP
579
n
106
ASP
579
C
PRO
580
n
107
PRO
580
C
TRP
581
n
108
TRP
581
C
ASN
582
n
109
ASN
582
C
CYS
583
n
110
CYS
583
C
TYR
584
n
111
TYR
584
C
MET
585
n
112
MET
585
C
CYS
586
n
113
CYS
586
C
GLY
587
n
114
GLY
587
C
HIS
588
n
115
HIS
588
C
LYS
589
n
116
LYS
589
C
GLY
590
n
117
GLY
590
C
THR
591
n
118
THR
591
C
TYR
592
n
119
TYR
592
C
GLY
593
n
120
GLY
593
C
LEU
594
n
121
LEU
594
C
LEU
595
n
122
LEU
595
C
ARG
596
n
123
ARG
596
C
ARG
597
n
124
ARG
597
C
ARG
598
n
125
ARG
598
C
GLU
599
n
126
GLU
599
C
ASP
600
n
127
ASP
600
C
TRP
601
n
128
TRP
601
C
PRO
602
n
129
PRO
602
C
SER
603
n
130
SER
603
C
ARG
604
n
131
ARG
604
C
LEU
605
n
132
LEU
605
C
GLN
606
n
133
GLN
606
C
MET
607
n
134
MET
607
C
PHE
608
n
135
PHE
608
C
PHE
609
n
136
PHE
609
C
ALA
610
n
137
ALA
610
C
ALA
1
n
1
ALA
1
P
ARG
2
n
2
ARG
2
P
THR
3
n
3
THR
3
P
LYS
4
n
4
LYS
4
P
GLN
5
n
5
GLN
5
P
THR
6
n
6
THR
6
P
ALA
7
n
7
ALA
7
P
ARG
8
n
8
ARG
8
P
author_and_software_defined_assembly
PISA
3
trimeric
2400
-9
14090
C
CYS
517
B
SG
CYS
44
1_555
C
ZN
703
I
ZN
ZN
1_555
C
CYS
494
B
SG
CYS
21
1_555
109.5
C
CYS
517
B
SG
CYS
44
1_555
C
ZN
703
I
ZN
ZN
1_555
C
CYS
497
B
SG
CYS
24
1_555
102.6
C
CYS
494
B
SG
CYS
21
1_555
C
ZN
703
I
ZN
ZN
1_555
C
CYS
497
B
SG
CYS
24
1_555
113.9
C
CYS
517
B
SG
CYS
44
1_555
C
ZN
703
I
ZN
ZN
1_555
C
CYS
514
B
SG
CYS
41
1_555
109.5
C
CYS
494
B
SG
CYS
21
1_555
C
ZN
703
I
ZN
ZN
1_555
C
CYS
514
B
SG
CYS
41
1_555
115.9
C
CYS
497
B
SG
CYS
24
1_555
C
ZN
703
I
ZN
ZN
1_555
C
CYS
514
B
SG
CYS
41
1_555
104.5
A
CYS
517
A
SG
CYS
44
1_555
A
ZN
703
F
ZN
ZN
1_555
A
CYS
494
A
SG
CYS
21
1_555
111.9
A
CYS
517
A
SG
CYS
44
1_555
A
ZN
703
F
ZN
ZN
1_555
A
CYS
514
A
SG
CYS
41
1_555
101.8
A
CYS
494
A
SG
CYS
21
1_555
A
ZN
703
F
ZN
ZN
1_555
A
CYS
514
A
SG
CYS
41
1_555
113.7
A
CYS
517
A
SG
CYS
44
1_555
A
ZN
703
F
ZN
ZN
1_555
A
CYS
497
A
SG
CYS
24
1_555
108.8
A
CYS
494
A
SG
CYS
21
1_555
A
ZN
703
F
ZN
ZN
1_555
A
CYS
497
A
SG
CYS
24
1_555
114.0
A
CYS
514
A
SG
CYS
41
1_555
A
ZN
703
F
ZN
ZN
1_555
A
CYS
497
A
SG
CYS
24
1_555
105.7
C
CYS
554
B
SG
CYS
81
1_555
C
ZN
701
G
ZN
ZN
1_555
C
CYS
549
B
SG
CYS
76
1_555
112.0
C
CYS
554
B
SG
CYS
81
1_555
C
ZN
701
G
ZN
ZN
1_555
C
CYS
583
B
SG
CYS
110
1_555
106.0
C
CYS
549
B
SG
CYS
76
1_555
C
ZN
701
G
ZN
ZN
1_555
C
CYS
583
B
SG
CYS
110
1_555
108.2
C
CYS
554
B
SG
CYS
81
1_555
C
ZN
701
G
ZN
ZN
1_555
C
CYS
586
B
SG
CYS
113
1_555
98.6
C
CYS
549
B
SG
CYS
76
1_555
C
ZN
701
G
ZN
ZN
1_555
C
CYS
586
B
SG
CYS
113
1_555
119.9
C
CYS
583
B
SG
CYS
110
1_555
C
ZN
701
G
ZN
ZN
1_555
C
CYS
586
B
SG
CYS
113
1_555
111.1
A
CYS
562
A
SG
CYS
89
1_555
A
ZN
702
E
ZN
ZN
1_555
A
CYS
540
A
SG
CYS
67
1_555
110.7
A
CYS
562
A
SG
CYS
89
1_555
A
ZN
702
E
ZN
ZN
1_555
A
CYS
537
A
SG
CYS
64
1_555
113.4
A
CYS
540
A
SG
CYS
67
1_555
A
ZN
702
E
ZN
ZN
1_555
A
CYS
537
A
SG
CYS
64
1_555
106.3
A
CYS
562
A
SG
CYS
89
1_555
A
ZN
702
E
ZN
ZN
1_555
A
CYS
559
A
SG
CYS
86
1_555
103.0
A
CYS
540
A
SG
CYS
67
1_555
A
ZN
702
E
ZN
ZN
1_555
A
CYS
559
A
SG
CYS
86
1_555
110.4
A
CYS
537
A
SG
CYS
64
1_555
A
ZN
702
E
ZN
ZN
1_555
A
CYS
559
A
SG
CYS
86
1_555
113.0
C
CYS
562
B
SG
CYS
89
1_555
C
ZN
702
H
ZN
ZN
1_555
C
CYS
559
B
SG
CYS
86
1_555
110.2
C
CYS
562
B
SG
CYS
89
1_555
C
ZN
702
H
ZN
ZN
1_555
C
CYS
537
B
SG
CYS
64
1_555
111.2
C
CYS
559
B
SG
CYS
86
1_555
C
ZN
702
H
ZN
ZN
1_555
C
CYS
537
B
SG
CYS
64
1_555
112.5
C
CYS
562
B
SG
CYS
89
1_555
C
ZN
702
H
ZN
ZN
1_555
C
CYS
540
B
SG
CYS
67
1_555
106.1
C
CYS
559
B
SG
CYS
86
1_555
C
ZN
702
H
ZN
ZN
1_555
C
CYS
540
B
SG
CYS
67
1_555
112.2
C
CYS
537
B
SG
CYS
64
1_555
C
ZN
702
H
ZN
ZN
1_555
C
CYS
540
B
SG
CYS
67
1_555
104.3
A
CYS
549
A
SG
CYS
76
1_555
A
ZN
701
D
ZN
ZN
1_555
A
CYS
586
A
SG
CYS
113
1_555
110.0
A
CYS
549
A
SG
CYS
76
1_555
A
ZN
701
D
ZN
ZN
1_555
A
CYS
554
A
SG
CYS
81
1_555
115.5
A
CYS
586
A
SG
CYS
113
1_555
A
ZN
701
D
ZN
ZN
1_555
A
CYS
554
A
SG
CYS
81
1_555
103.9
A
CYS
549
A
SG
CYS
76
1_555
A
ZN
701
D
ZN
ZN
1_555
A
CYS
583
A
SG
CYS
110
1_555
110.6
A
CYS
586
A
SG
CYS
113
1_555
A
ZN
701
D
ZN
ZN
1_555
A
CYS
583
A
SG
CYS
110
1_555
113.7
A
CYS
554
A
SG
CYS
81
1_555
A
ZN
701
D
ZN
ZN
1_555
A
CYS
583
A
SG
CYS
110
1_555
103.0
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
LEU
504
A
N
LEU
31
A
O
MET
513
A
O
MET
40
A
N
LEU
547
A
N
LEU
74
A
O
PHE
558
A
O
PHE
85
A
N
TYR
592
A
N
TYR
119
A
O
LEU
595
A
O
LEU
122
C
N
LEU
504
B
N
LEU
31
C
O
MET
513
B
O
MET
40
C
O
PHE
558
B
O
PHE
85
C
N
LEU
547
B
N
LEU
74
C
N
VAL
546
B
N
VAL
73
P
O
LYS
4
C
O
LYS
4
C
N
TYR
592
B
N
TYR
119
C
O
LEU
595
B
O
LEU
122
1
A
A
O
O
HOH
HOH
848
849
1.93
1
A
A
O
O
HOH
HOH
806
843
1.95
1
A
A
O
O
HOH
HOH
821
836
2.02
1
A
A
NH2
O
ARG
HOH
596
838
2.14
1
A
A
OE1
NH2
GLU
ARG
505
604
2.19
1
A
ARG
544
-95.19
-101.44
1
A
CYS
554
-121.68
-71.21
1
A
LYS
577
-93.54
48.71
1
C
CYS
497
-143.16
-16.27
1
C
ARG
544
-96.38
-73.02
1
C
ASN
552
54.43
-93.34
1
C
ASN
553
-67.94
9.69
1
C
CYS
554
-103.20
-69.40
1
C
PRO
580
-74.89
-155.63
1
C
PHE
609
-91.78
45.85
1
P
ALA
7
-112.58
74.17
0.2304
0.1736
0.1764
2.406
41.557
497
10420
10329
4.81
99.13
0.28
RANDOM
1
1.38
MOLECULAR REPLACEMENT
23.92
0.90
1.11
ML
FLAT BULK SOLVENT MODEL
2.406
41.557
104
2299
6
0
2189
0.009
2235
1.262
3012
18.089
827
0.082
312
0.004
401
0.2954
0.2096
2.6485
121
2368
4
97.00
0.2693
0.1982
3.0316
124
2479
4
100.00
0.2172
0.1687
3.8191
129
2465
4
100.00
0.2031
0.1556
41.5627
123
2520
4
100.00
2.4
50
4QBQ
10349
-3
-3
0.117
1
4.8
99.9
2.40
2.46
1
99.4
2.46
2.52
1
99.6
2.52
2.59
1
100.0
2.59
2.66
1
100.0
2.66
2.75
1
100.0
2.75
2.85
1
100.0
2.85
2.96
1
100.0
2.96
3.09
1
100.0
3.09
3.26
1
99.9
3.26
3.46
1
100.0
3.46
3.73
1
100.0
3.73
4.10
1
100.0
4.10
4.70
1
100.0
4.70
5.92
1
100.0
5.92
50.00
1
100.0
data collection
HKL-2000
phasing
MOLREP
refinement
PHENIX
(phenix.refine: 1.8.2_1309)
data reduction
HKL-2000
data scaling
HKL-2000
DNA (cytosine-5)-methyltransferase 3A (E.C.2.1.1.37), Histone H3
Crystal structure of DNMT3a ADD domain bound to H3 peptide
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
3
N
N
4
N
N
4
N
N
4
N
N
A
GLY
474
A
GLY
1
HELX_P
A
GLN
485
A
GLN
12
1
1
12
A
ASN
489
A
ASN
16
HELX_P
A
ILE
493
A
ILE
20
5
2
5
A
CYS
514
A
CYS
41
HELX_P
A
ALA
525
A
ALA
52
1
3
12
A
VAL
560
A
VAL
87
HELX_P
A
VAL
567
A
VAL
94
1
4
8
A
GLY
570
A
GLY
97
HELX_P
A
LYS
577
A
LYS
104
1
5
8
A
ASP
600
A
ASP
127
HELX_P
A
PHE
609
A
PHE
136
1
6
10
C
PRO
475
B
PRO
2
HELX_P
C
GLN
485
B
GLN
12
1
7
11
C
ASN
489
B
ASN
16
HELX_P
C
ILE
493
B
ILE
20
5
8
5
C
CYS
514
B
CYS
41
HELX_P
C
CYS
524
B
CYS
51
1
9
11
C
VAL
560
B
VAL
87
HELX_P
C
VAL
567
B
VAL
94
1
10
8
C
GLY
570
B
GLY
97
HELX_P
C
GLU
578
B
GLU
105
1
11
9
C
ASP
600
B
ASP
127
HELX_P
C
PHE
609
B
PHE
136
1
12
10
disulf
2.032
C
CYS
524
B
SG
CYS
51
1_555
C
CYS
541
B
SG
CYS
68
1_555
metalc
2.382
C
CYS
517
B
SG
CYS
44
1_555
C
ZN
703
I
ZN
ZN
1_555
metalc
2.387
C
CYS
494
B
SG
CYS
21
1_555
C
ZN
703
I
ZN
ZN
1_555
metalc
2.397
A
CYS
517
A
SG
CYS
44
1_555
A
ZN
703
F
ZN
ZN
1_555
metalc
2.420
C
CYS
554
B
SG
CYS
81
1_555
C
ZN
701
G
ZN
ZN
1_555
metalc
2.424
A
CYS
562
A
SG
CYS
89
1_555
A
ZN
702
E
ZN
ZN
1_555
metalc
2.435
C
CYS
549
B
SG
CYS
76
1_555
C
ZN
701
G
ZN
ZN
1_555
metalc
2.457
C
CYS
562
B
SG
CYS
89
1_555
C
ZN
702
H
ZN
ZN
1_555
metalc
2.465
A
CYS
540
A
SG
CYS
67
1_555
A
ZN
702
E
ZN
ZN
1_555
metalc
2.466
C
CYS
559
B
SG
CYS
86
1_555
C
ZN
702
H
ZN
ZN
1_555
metalc
2.473
A
CYS
549
A
SG
CYS
76
1_555
A
ZN
701
D
ZN
ZN
1_555
metalc
2.480
A
CYS
586
A
SG
CYS
113
1_555
A
ZN
701
D
ZN
ZN
1_555
metalc
2.486
A
CYS
537
A
SG
CYS
64
1_555
A
ZN
702
E
ZN
ZN
1_555
metalc
2.488
A
CYS
559
A
SG
CYS
86
1_555
A
ZN
702
E
ZN
ZN
1_555
metalc
2.491
A
CYS
494
A
SG
CYS
21
1_555
A
ZN
703
F
ZN
ZN
1_555
metalc
2.515
C
CYS
537
B
SG
CYS
64
1_555
C
ZN
702
H
ZN
ZN
1_555
metalc
2.519
A
CYS
514
A
SG
CYS
41
1_555
A
ZN
703
F
ZN
ZN
1_555
metalc
2.520
A
CYS
554
A
SG
CYS
81
1_555
A
ZN
701
D
ZN
ZN
1_555
metalc
2.526
A
CYS
583
A
SG
CYS
110
1_555
A
ZN
701
D
ZN
ZN
1_555
metalc
2.530
C
CYS
497
B
SG
CYS
24
1_555
C
ZN
703
I
ZN
ZN
1_555
metalc
2.536
A
CYS
497
A
SG
CYS
24
1_555
A
ZN
703
F
ZN
ZN
1_555
metalc
2.553
C
CYS
540
B
SG
CYS
67
1_555
C
ZN
702
H
ZN
ZN
1_555
metalc
2.556
C
CYS
514
B
SG
CYS
41
1_555
C
ZN
703
I
ZN
ZN
1_555
metalc
2.566
C
CYS
583
B
SG
CYS
110
1_555
C
ZN
701
G
ZN
ZN
1_555
metalc
2.587
C
CYS
586
B
SG
CYS
113
1_555
C
ZN
701
G
ZN
ZN
1_555
TRANSFERASE
Zinc Finger, Histone Binding, TRANSFERASE
A
ASP
579
A
ASP
106
1
A
PRO
580
A
PRO
107
-4.83
C
ASP
579
B
ASP
106
1
C
PRO
580
B
PRO
107
-4.19
DNM3A_HUMAN
UNP
1
479
Q9Y6K1
LVYEVRQKCRNIEDICISCGSLNVTLEHPLFVGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCF
CVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRREDWPSRLQMFFA
4QBQ
PDB
2
4QBQ
479
610
4QBQ
479
610
Q9Y6K1
A
1
6
137
479
610
4QBQ
479
610
Q9Y6K1
C
1
6
137
1
8
4QBQ
1
8
4QBQ
P
2
1
8
1
EXPRESSION TAG
GLY
474
4QBQ
A
Q9Y6K1
UNP
1
1
EXPRESSION TAG
PRO
475
4QBQ
A
Q9Y6K1
UNP
2
1
EXPRESSION TAG
LEU
476
4QBQ
A
Q9Y6K1
UNP
3
1
EXPRESSION TAG
GLY
477
4QBQ
A
Q9Y6K1
UNP
4
1
EXPRESSION TAG
SER
478
4QBQ
A
Q9Y6K1
UNP
5
2
EXPRESSION TAG
GLY
474
4QBQ
C
Q9Y6K1
UNP
1
2
EXPRESSION TAG
PRO
475
4QBQ
C
Q9Y6K1
UNP
2
2
EXPRESSION TAG
LEU
476
4QBQ
C
Q9Y6K1
UNP
3
2
EXPRESSION TAG
GLY
477
4QBQ
C
Q9Y6K1
UNP
4
2
EXPRESSION TAG
SER
478
4QBQ
C
Q9Y6K1
UNP
5
2
2
2
2
3
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LEU
504
A
LEU
31
A
GLU
505
A
GLU
32
A
GLY
512
A
GLY
39
A
MET
513
A
MET
40
A
VAL
546
A
VAL
73
A
MET
548
A
MET
75
A
CYS
557
A
CYS
84
A
CYS
559
A
CYS
86
A
THR
591
A
THR
118
A
TYR
592
A
TYR
119
A
LEU
595
A
LEU
122
A
ARG
596
A
ARG
123
C
LEU
504
B
LEU
31
C
GLU
505
B
GLU
32
C
GLY
512
B
GLY
39
C
MET
513
B
MET
40
C
CYS
557
B
CYS
84
C
CYS
559
B
CYS
86
C
GLU
545
B
GLU
72
C
MET
548
B
MET
75
P
THR
3
C
THR
3
P
GLN
5
C
GLN
5
C
THR
591
B
THR
118
C
TYR
592
B
TYR
119
C
LEU
595
B
LEU
122
C
ARG
596
B
ARG
123
BINDING SITE FOR RESIDUE ZN A 701
Software
4
BINDING SITE FOR RESIDUE ZN A 702
Software
4
BINDING SITE FOR RESIDUE ZN A 703
Software
4
BINDING SITE FOR RESIDUE ZN C 701
Software
4
BINDING SITE FOR RESIDUE ZN C 702
Software
4
BINDING SITE FOR RESIDUE ZN C 703
Software
4
A
CYS
549
A
CYS
76
4
1_555
A
CYS
554
A
CYS
81
4
1_555
A
CYS
583
A
CYS
110
4
1_555
A
CYS
586
A
CYS
113
4
1_555
A
CYS
537
A
CYS
64
4
1_555
A
CYS
540
A
CYS
67
4
1_555
A
CYS
559
A
CYS
86
4
1_555
A
CYS
562
A
CYS
89
4
1_555
A
CYS
494
A
CYS
21
4
1_555
A
CYS
497
A
CYS
24
4
1_555
A
CYS
514
A
CYS
41
4
1_555
A
CYS
517
A
CYS
44
4
1_555
C
CYS
549
B
CYS
76
4
1_555
C
CYS
554
B
CYS
81
4
1_555
C
CYS
583
B
CYS
110
4
1_555
C
CYS
586
B
CYS
113
4
1_555
C
CYS
537
B
CYS
64
4
1_555
C
CYS
540
B
CYS
67
4
1_555
C
CYS
559
B
CYS
86
4
1_555
C
CYS
562
B
CYS
89
4
1_555
C
CYS
494
B
CYS
21
4
1_555
C
CYS
497
B
CYS
24
4
1_555
C
CYS
514
B
CYS
41
4
1_555
C
CYS
517
B
CYS
44
4
1_555
4
P 1 21 1