0.011227
0.000000
0.000000
0.000000
0.010528
0.000000
0.000000
0.000000
0.018269
0.00000
0.00000
0.00000
Otani, J.
Arita, K.
Kato, T.
Kinoshita, M.
Ariyoshi, M.
Shirakawa, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
89.074
94.989
54.738
C10 H16 N3 O7 P
321.224
n
5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
DNA linking
C2 H3 O2 -1
59.044
ACETATE ION
non-polymer
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
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C2 H6 O2
62.068
1,2-ETHANEDIOL
ETHYLENE GLYCOL
non-polymer
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
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
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
288
6351
6362
10.1074/jbc.M112.431098
23316048
Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4
2013
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
95
1
95
2
CCD
2010-01-27
ADSC QUANTUM 210r
CCD
2009-10-14
ADSC QUANTUM 270
SINGLE WAVELENGTH
M
x-ray
1
SINGLE WAVELENGTH
M
x-ray
2
1.000
1.0
1.0
BL-5A
Photon Factory
1.000
SYNCHROTRON
PHOTON FACTORY BEAMLINE BL-5A
AR-NE3A
Photon Factory
SYNCHROTRON
PHOTON FACTORY BEAMLINE AR-NE3A
7829.089
Methyl-CpG-binding domain protein 4
3.2.2.-
methyl CpG binding domain, UNP residues 69-136
1
man
polymer
4263.809
DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP*A)-3')
1
syn
polymer
4326.812
DNA (5'-D(*GP*TP*CP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3')
1
syn
polymer
59.044
ACETATE ION
3
syn
non-polymer
62.068
1,2-ETHANEDIOL
6
syn
non-polymer
18.015
water
154
nat
water
Methyl-CpG-binding protein MBD4, Mismatch-specific DNA N-glycosylase
no
no
SGHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG
SGHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG
A
polypeptide(L)
no
yes
(DG)(DT)(DC)(DA)(DC)(DT)(DA)(DC)(5CM)(DG)(DG)(DA)(DC)(DA)
GTCACTACCGGACA
B
polydeoxyribonucleotide
no
no
(DG)(DT)(DC)(DT)(DG)(DG)(DT)(DA)(DG)(DT)(DG)(DA)(DC)(DT)
GTCTGGTAGTGACT
C
polydeoxyribonucleotide
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
mouse
sample
Mbd4
10090
Mus musculus
562
Escherichia coli
BL21(DE3)
plasmid
2
3.53
65.11
VAPOR DIFFUSION, HANGING DROP
4.4
pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
VAPOR DIFFUSION, HANGING DROP
4.4
pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
-25.080
1
19
B
1
C
13
-0.391
B_DG1:DC13_C
1
-16.480
-0.225
-0.118
0.035
-10.782
1
20
B
2
C
12
-3.304
B_DT2:DA12_C
2
-7.031
-0.347
0.089
-0.073
-6.211
1
19
B
3
C
11
-1.076
B_DC3:DG11_C
3
-6.081
-0.101
-0.062
-0.219
4.348
1
20
B
4
C
10
0.624
B_DA4:DT10_C
4
-9.707
0.201
0.118
-0.153
4.055
1
19
B
5
C
9
3.769
B_DC5:DG9_C
5
-13.621
0.793
0.117
-0.245
-4.552
1
20
B
6
C
8
1.097
B_DT6:DA8_C
6
-9.780
-0.128
0.127
-0.240
-9.820
1
20
B
7
C
7
0.271
B_DA7:DT7_C
7
-7.266
0.122
0.064
-0.145
-5.872
1
19
B
8
C
6
-1.499
B_DC8:DG6_C
8
-3.950
0.330
0.193
-0.147
-3.950
1
19
B
9
C
5
-0.557
B_5CM9:DG5_C
9
-7.467
0.357
-0.032
-0.134
13.254
1
28
B
10
C
4
-7.293
B_DG10:DT4_C
10
9.223
-2.431
0.269
-0.584
27.737
1
19
B
11
C
3
0.181
B_DG11:DC3_C
11
-0.384
-0.238
0.287
-0.044
24.158
1
20
B
12
C
2
2.402
B_DA12:DT2_C
12
-17.695
0.149
0.179
-0.058
13.623
1
19
B
13
C
1
0.122
B_DC13:DG1_C
13
-15.089
0.334
-0.142
-0.069
2.850
31.960
B
B
1
2
6.193
C
C
13
12
2.897
3.402
-0.896
-0.664
BB_DG1DT2:DA12DC13_CC
1
-1.467
2.670
31.750
-1.748
1.393
3.206
37.740
B
B
2
3
5.653
C
C
12
11
3.168
3.647
0.751
0.019
BB_DT2DC3:DG11DA12_CC
2
3.142
-4.870
37.443
-0.432
-0.763
2.993
30.182
B
B
3
4
16.977
C
C
11
10
3.073
8.717
-0.081
0.160
BB_DC3DA4:DT10DG11_CC
3
-1.289
2.511
28.896
-1.375
-0.093
3.212
33.801
B
B
4
5
5.116
C
C
10
9
3.278
2.971
0.874
-0.725
BB_DA4DC5:DG9DT10_CC
4
0.323
-0.556
33.673
-1.725
-1.452
3.277
32.760
B
B
5
6
8.348
C
C
9
8
3.410
4.682
0.124
-0.653
BB_DC5DT6:DA8DG9_CC
5
3.923
-6.994
32.201
-1.990
0.477
3.176
32.985
B
B
6
7
13.581
C
C
8
7
3.400
7.643
-0.073
-0.589
BB_DT6DA7:DT7DA8_CC
6
0.991
-1.760
32.096
-2.361
0.300
3.221
34.093
B
B
7
8
4.272
C
C
7
6
3.273
2.502
-0.537
-0.554
BB_DA7DC8:DG6DT7_CC
7
0.222
-0.379
34.003
-1.341
0.951
3.390
30.934
B
B
8
9
-3.241
C
C
6
5
3.336
-1.725
0.743
-0.060
BB_DC85CM9:DG5DG6_CC
8
3.086
-5.797
30.736
0.232
-0.777
3.099
28.816
B
B
9
10
-8.665
C
C
5
4
3.204
-4.268
0.110
-0.096
BB_5CM9DG10:DT4DG5_CC
9
-5.786
11.745
27.923
0.742
-1.486
3.139
35.792
B
B
10
11
-1.301
C
C
4
3
3.177
-0.798
0.296
-0.729
BB_DG10DG11:DC3DT4_CC
10
-4.143
6.756
35.551
-1.074
-1.059
3.423
37.971
B
B
11
12
6.114
C
C
3
2
3.434
3.962
-0.893
-0.723
BB_DG11DA12:DT2DC3_CC
11
-4.511
6.960
37.510
-1.645
0.765
3.250
33.683
B
B
12
13
9.118
C
C
2
1
3.498
5.261
0.197
-1.291
BB_DA12DC13:DG1DT2_CC
12
-1.517
2.629
33.248
-3.118
-0.596
repository
Initial release
Database references
1
0
2013-01-16
1
1
2013-08-14
PDBJ
Y
PDBJ
2012-09-21
REL
REL
ACT
ACETATE ION
EDO
1,2-ETHANEDIOL
HOH
water
ACT
2
4
ACT
ACT
201
A
ACT
3
4
ACT
ACT
202
A
EDO
11
5
EDO
EDO
203
A
EDO
12
5
EDO
EDO
204
A
EDO
13
5
EDO
EDO
205
A
EDO
14
5
EDO
EDO
206
A
EDO
21
5
EDO
EDO
207
A
ACT
1
4
ACT
ACT
101
B
EDO
19
5
EDO
EDO
101
C
HOH
2
6
HOH
HOH
301
A
HOH
3
6
HOH
HOH
302
A
HOH
4
6
HOH
HOH
303
A
HOH
6
6
HOH
HOH
304
A
HOH
7
6
HOH
HOH
305
A
HOH
8
6
HOH
HOH
306
A
HOH
10
6
HOH
HOH
307
A
HOH
12
6
HOH
HOH
308
A
HOH
14
6
HOH
HOH
309
A
HOH
15
6
HOH
HOH
310
A
HOH
18
6
HOH
HOH
311
A
HOH
19
6
HOH
HOH
312
A
HOH
23
6
HOH
HOH
313
A
HOH
26
6
HOH
HOH
314
A
HOH
29
6
HOH
HOH
315
A
HOH
36
6
HOH
HOH
316
A
HOH
39
6
HOH
HOH
317
A
HOH
42
6
HOH
HOH
318
A
HOH
43
6
HOH
HOH
319
A
HOH
46
6
HOH
HOH
320
A
HOH
48
6
HOH
HOH
321
A
HOH
49
6
HOH
HOH
322
A
HOH
50
6
HOH
HOH
323
A
HOH
53
6
HOH
HOH
324
A
HOH
57
6
HOH
HOH
325
A
HOH
60
6
HOH
HOH
326
A
HOH
63
6
HOH
HOH
327
A
HOH
69
6
HOH
HOH
328
A
HOH
70
6
HOH
HOH
329
A
HOH
71
6
HOH
HOH
330
A
HOH
75
6
HOH
HOH
331
A
HOH
80
6
HOH
HOH
332
A
HOH
81
6
HOH
HOH
333
A
HOH
82
6
HOH
HOH
334
A
HOH
91
6
HOH
HOH
335
A
HOH
96
6
HOH
HOH
336
A
HOH
97
6
HOH
HOH
337
A
HOH
99
6
HOH
HOH
338
A
HOH
100
6
HOH
HOH
339
A
HOH
101
6
HOH
HOH
340
A
HOH
102
6
HOH
HOH
341
A
HOH
105
6
HOH
HOH
342
A
HOH
106
6
HOH
HOH
343
A
HOH
107
6
HOH
HOH
344
A
HOH
112
6
HOH
HOH
345
A
HOH
117
6
HOH
HOH
346
A
HOH
123
6
HOH
HOH
347
A
HOH
126
6
HOH
HOH
348
A
HOH
129
6
HOH
HOH
349
A
HOH
130
6
HOH
HOH
350
A
HOH
131
6
HOH
HOH
351
A
HOH
133
6
HOH
HOH
352
A
HOH
137
6
HOH
HOH
353
A
HOH
139
6
HOH
HOH
354
A
HOH
141
6
HOH
HOH
355
A
HOH
143
6
HOH
HOH
356
A
HOH
144
6
HOH
HOH
357
A
HOH
148
6
HOH
HOH
358
A
HOH
149
6
HOH
HOH
359
A
HOH
151
6
HOH
HOH
360
A
HOH
152
6
HOH
HOH
361
A
HOH
9
6
HOH
HOH
362
A
HOH
13
6
HOH
HOH
201
B
HOH
16
6
HOH
HOH
202
B
HOH
20
6
HOH
HOH
203
B
HOH
21
6
HOH
HOH
204
B
HOH
22
6
HOH
HOH
205
B
HOH
27
6
HOH
HOH
206
B
HOH
28
6
HOH
HOH
207
B
HOH
31
6
HOH
HOH
208
B
HOH
33
6
HOH
HOH
209
B
HOH
35
6
HOH
HOH
210
B
HOH
38
6
HOH
HOH
211
B
HOH
41
6
HOH
HOH
212
B
HOH
44
6
HOH
HOH
213
B
HOH
54
6
HOH
HOH
214
B
HOH
59
6
HOH
HOH
215
B
HOH
61
6
HOH
HOH
216
B
HOH
65
6
HOH
HOH
217
B
HOH
66
6
HOH
HOH
218
B
HOH
67
6
HOH
HOH
219
B
HOH
68
6
HOH
HOH
220
B
HOH
73
6
HOH
HOH
221
B
HOH
76
6
HOH
HOH
222
B
HOH
77
6
HOH
HOH
223
B
HOH
83
6
HOH
HOH
224
B
HOH
84
6
HOH
HOH
225
B
HOH
87
6
HOH
HOH
226
B
HOH
89
6
HOH
HOH
227
B
HOH
90
6
HOH
HOH
228
B
HOH
92
6
HOH
HOH
229
B
HOH
94
6
HOH
HOH
230
B
HOH
95
6
HOH
HOH
231
B
HOH
108
6
HOH
HOH
232
B
HOH
110
6
HOH
HOH
233
B
HOH
111
6
HOH
HOH
234
B
HOH
113
6
HOH
HOH
235
B
HOH
114
6
HOH
HOH
236
B
HOH
115
6
HOH
HOH
237
B
HOH
116
6
HOH
HOH
238
B
HOH
119
6
HOH
HOH
239
B
HOH
120
6
HOH
HOH
240
B
HOH
127
6
HOH
HOH
241
B
HOH
128
6
HOH
HOH
242
B
HOH
132
6
HOH
HOH
243
B
HOH
134
6
HOH
HOH
244
B
HOH
135
6
HOH
HOH
245
B
HOH
138
6
HOH
HOH
246
B
HOH
146
6
HOH
HOH
247
B
HOH
147
6
HOH
HOH
248
B
HOH
153
6
HOH
HOH
249
B
HOH
154
6
HOH
HOH
250
B
HOH
11
6
HOH
HOH
251
B
HOH
40
6
HOH
HOH
201
C
HOH
1
6
HOH
HOH
202
C
HOH
5
6
HOH
HOH
203
C
HOH
17
6
HOH
HOH
204
C
HOH
24
6
HOH
HOH
205
C
HOH
25
6
HOH
HOH
206
C
HOH
30
6
HOH
HOH
207
C
HOH
32
6
HOH
HOH
208
C
HOH
34
6
HOH
HOH
209
C
HOH
37
6
HOH
HOH
210
C
HOH
45
6
HOH
HOH
211
C
HOH
47
6
HOH
HOH
212
C
HOH
51
6
HOH
HOH
213
C
HOH
52
6
HOH
HOH
214
C
HOH
55
6
HOH
HOH
215
C
HOH
56
6
HOH
HOH
216
C
HOH
58
6
HOH
HOH
217
C
HOH
62
6
HOH
HOH
218
C
HOH
64
6
HOH
HOH
219
C
HOH
72
6
HOH
HOH
220
C
HOH
74
6
HOH
HOH
221
C
HOH
78
6
HOH
HOH
222
C
HOH
79
6
HOH
HOH
223
C
HOH
85
6
HOH
HOH
224
C
HOH
86
6
HOH
HOH
225
C
HOH
88
6
HOH
HOH
226
C
HOH
93
6
HOH
HOH
227
C
HOH
98
6
HOH
HOH
228
C
HOH
103
6
HOH
HOH
229
C
HOH
104
6
HOH
HOH
230
C
HOH
109
6
HOH
HOH
231
C
HOH
118
6
HOH
HOH
232
C
HOH
121
6
HOH
HOH
233
C
HOH
122
6
HOH
HOH
234
C
HOH
124
6
HOH
HOH
235
C
HOH
125
6
HOH
HOH
236
C
HOH
136
6
HOH
HOH
237
C
HOH
140
6
HOH
HOH
238
C
HOH
142
6
HOH
HOH
239
C
HOH
145
6
HOH
HOH
240
C
HOH
150
6
HOH
HOH
241
C
n
1
68
A
n
2
69
A
n
3
70
A
LYS
71
n
4
LYS
71
A
PRO
72
n
5
PRO
72
A
VAL
73
n
6
VAL
73
A
PRO
74
n
7
PRO
74
A
CYS
75
n
8
CYS
75
A
GLY
76
n
9
GLY
76
A
TRP
77
n
10
TRP
77
A
GLU
78
n
11
GLU
78
A
ARG
79
n
12
ARG
79
A
VAL
80
n
13
VAL
80
A
VAL
81
n
14
VAL
81
A
LYS
82
n
15
LYS
82
A
GLN
83
n
16
GLN
83
A
ARG
84
n
17
ARG
84
A
LEU
85
n
18
LEU
85
A
SER
86
n
19
SER
86
A
GLY
87
n
20
GLY
87
A
LYS
88
n
21
LYS
88
A
THR
89
n
22
THR
89
A
ALA
90
n
23
ALA
90
A
GLY
91
n
24
GLY
91
A
LYS
92
n
25
LYS
92
A
PHE
93
n
26
PHE
93
A
ASP
94
n
27
ASP
94
A
VAL
95
n
28
VAL
95
A
TYR
96
n
29
TYR
96
A
PHE
97
n
30
PHE
97
A
ILE
98
n
31
ILE
98
A
SER
99
n
32
SER
99
A
PRO
100
n
33
PRO
100
A
GLN
101
n
34
GLN
101
A
GLY
102
n
35
GLY
102
A
LEU
103
n
36
LEU
103
A
LYS
104
n
37
LYS
104
A
PHE
105
n
38
PHE
105
A
ARG
106
n
39
ARG
106
A
SER
107
n
40
SER
107
A
LYS
108
n
41
LYS
108
A
ARG
109
n
42
ARG
109
A
SER
110
n
43
SER
110
A
LEU
111
n
44
LEU
111
A
ALA
112
n
45
ALA
112
A
ASN
113
n
46
ASN
113
A
TYR
114
n
47
TYR
114
A
LEU
115
n
48
LEU
115
A
LEU
116
n
49
LEU
116
A
LYS
117
n
50
LYS
117
A
ASN
118
n
51
ASN
118
A
GLY
119
n
52
GLY
119
A
GLU
120
n
53
GLU
120
A
THR
121
n
54
THR
121
A
PHE
122
n
55
PHE
122
A
LEU
123
n
56
LEU
123
A
LYS
124
n
57
LYS
124
A
PRO
125
n
58
PRO
125
A
GLU
126
n
59
GLU
126
A
ASP
127
n
60
ASP
127
A
PHE
128
n
61
PHE
128
A
ASN
129
n
62
ASN
129
A
PHE
130
n
63
PHE
130
A
THR
131
n
64
THR
131
A
VAL
132
n
65
VAL
132
A
LEU
133
n
66
LEU
133
A
PRO
134
n
67
PRO
134
A
LYS
135
n
68
LYS
135
A
n
69
136
A
DG
1
n
1
DG
1
B
DT
2
n
2
DT
2
B
DC
3
n
3
DC
3
B
DA
4
n
4
DA
4
B
DC
5
n
5
DC
5
B
DT
6
n
6
DT
6
B
DA
7
n
7
DA
7
B
DC
8
n
8
DC
8
B
5CM
9
n
9
5CM
9
B
DG
10
n
10
DG
10
B
DG
11
n
11
DG
11
B
DA
12
n
12
DA
12
B
DC
13
n
13
DC
13
B
DA
14
n
14
DA
14
B
DG
1
n
1
DG
1
C
DT
2
n
2
DT
2
C
DC
3
n
3
DC
3
C
DT
4
n
4
DT
4
C
DG
5
n
5
DG
5
C
DG
6
n
6
DG
6
C
DT
7
n
7
DT
7
C
DA
8
n
8
DA
8
C
DG
9
n
9
DG
9
C
DT
10
n
10
DT
10
C
DG
11
n
11
DG
11
C
DA
12
n
12
DA
12
C
DC
13
n
13
DC
13
C
DT
14
n
14
DT
14
C
0.6284
-0.4314
0.3256
0.9797
-0.6242
1.5410
0.0083
-0.0141
0.0059
-0.0971
0.0234
-0.0729
0.0997
-0.0137
-0.0487
0.2326
-0.0073
0.0026
0.2517
-0.0245
0.2424
refined
-3.3944
-11.8131
4.3750
X-RAY DIFFRACTION
1.7749
1.6014
-0.4628
2.1899
-1.0130
0.5161
-0.0418
-0.2728
0.2781
-0.2738
-0.0546
0.3679
0.1146
0.2262
0.0383
0.3457
-0.0759
-0.0226
0.3937
-0.1141
0.3550
refined
-18.9331
-12.0063
-13.7962
X-RAY DIFFRACTION
3.7803
0.2987
0.0373
0.6264
0.3534
0.3422
-0.2650
0.0063
-0.3741
-0.1841
0.1125
0.1463
0.0021
-0.1157
0.1730
0.3022
-0.0426
-0.0095
0.4634
-0.0021
0.3583
refined
-22.6605
-13.3668
-11.2981
X-RAY DIFFRACTION
A
71
A
135
X-RAY DIFFRACTION
1
chain A
B
1
B
14
X-RAY DIFFRACTION
2
chain B
C
1
C
14
X-RAY DIFFRACTION
3
chain C
author_and_software_defined_assembly
PISA
3
trimeric
4670
-8
10660
B
5CM
9
B
5CM
9
DC
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
VAL
80
A
N
VAL
13
A
O
TYR
96
A
O
TYR
29
A
N
PHE
97
A
N
PHE
30
A
O
PHE
105
A
O
PHE
38
1
A
HOH
320
M
HOH
1
B
HOH
201
N
HOH
1
A
CG
LYS
71
A
CG
LYS
4
1
Y
1
A
CD
LYS
71
A
CD
LYS
4
1
Y
1
A
CE
LYS
71
A
CE
LYS
4
1
Y
1
A
NZ
LYS
71
A
NZ
LYS
4
1
Y
1
A
SER
68
A
SER
1
1
Y
1
A
GLY
69
A
GLY
2
1
Y
1
A
HIS
70
A
HIS
3
1
Y
1
A
GLY
136
A
GLY
69
1
Y
1
B
B
OP2
O
DA
HOH
4
237
2.19
1
-4.55
0.50
120.30
115.75
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
79
79
79
N
1
3.62
0.50
120.30
123.92
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
79
79
79
N
1
5.79
0.50
106.80
112.59
B
B
B
O4'
C1'
C2'
DG
DG
DG
1
1
1
N
1
1.91
0.30
108.30
110.21
B
B
B
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
4.33
0.70
121.90
126.23
B
B
B
N3
C2
O2
DC
DC
DC
5
5
5
N
1
5.71
0.60
119.00
124.71
B
B
B
C4
C5
C7
DT
DT
DT
6
6
6
N
1
-5.17
0.60
122.90
117.73
B
B
B
C6
C5
C7
DT
DT
DT
6
6
6
N
1
-4.73
0.70
108.00
103.27
B
B
B
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
4.71
0.30
108.30
113.01
B
B
B
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
9.80
1.50
119.60
129.40
B
B
B
OP1
P
OP2
DA
DA
DA
14
14
14
N
1
-2.92
0.40
104.50
101.58
B
B
B
O4'
C4'
C3'
DA
DA
DA
14
14
14
N
1
-5.52
0.80
102.40
96.88
B
B
B
C3'
C2'
C1'
DA
DA
DA
14
14
14
N
1
3.33
0.50
106.80
110.13
B
B
B
O4'
C1'
C2'
DA
DA
DA
14
14
14
N
1
2.26
0.30
108.30
110.56
C
C
C
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
-3.66
0.60
127.20
123.54
C
C
C
C2
N3
C4
DT
DT
DT
2
2
2
N
1
-3.62
0.60
123.70
120.08
C
C
C
C5
C6
N1
DT
DT
DT
2
2
2
N
1
-3.16
0.50
119.90
116.74
C
C
C
C2
N3
C4
DC
DC
DC
3
3
3
N
1
-3.13
0.50
121.00
117.87
C
C
C
C5
C6
N1
DC
DC
DC
3
3
3
N
1
6.08
0.30
108.30
114.38
C
C
C
O4'
C1'
N1
DT
DT
DT
4
4
4
N
1
3.35
0.50
111.50
114.85
C
C
C
C5
C6
N1
DG
DG
DG
5
5
5
N
1
-8.42
1.00
110.10
101.68
C
C
C
C1'
O4'
C4'
DG
DG
DG
11
11
11
N
1
-4.86
0.80
102.40
97.54
C
C
C
C3'
C2'
C1'
DG
DG
DG
11
11
11
N
1
2.30
0.30
108.30
110.60
C
C
C
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
-4.43
0.70
124.90
120.47
C
C
C
C5
C4
O4
DT
DT
DT
14
14
14
N
1
B
B
O3'
C3'
DG
DG
11
11
-0.051
0.006
1.419
1.368
N
1
B
B
C6
N1
DA
DA
14
14
0.043
0.007
1.351
1.394
N
84.750
40.4743
22.070
-12.9528
0.0000
0.0000
10.7675
-0.0000
2.1853
0.2235
0.1875
0.1892
2.00
23.747
801
16002
5.01
99.44
1.000
0.500
0.30
1
1.34
SAD
24.6200
0.86
1.10
ML
FLAT BULK SOLVENT MODEL
54.253
0.342
2.00
23.747
154
1285
36
570
525
0.018
1205
2.071
1728
23.326
479
0.119
185
0.010
123
0.2707
0.2332
2.1240
150
2475
2625
6
100.0000
0.3677
0.2553
2.2879
139
2493
2632
6
99.0000
0.2924
0.2338
2.5179
148
2500
2648
6
100.0000
0.2713
0.2178
2.8817
125
2545
2670
6
100.0000
0.2235
0.1711
3.6286
117
2566
2683
6
100.0000
0.1633
0.1626
23.7489
122
2622
2744
6
98.0000
36.360
2.0
50
3VXV
16110
16062
1
1
0.031
1,2
18.2
7.2
99.7
0.365
2.00
2.07
4.3
1,2
7.3
100
data collection
HKL-2000
phasing
SOLVE
refinement
PHENIX
(phenix.refine: 1.6.4_486)
data reduction
HKL-2000
data scaling
HKL-2000
Methyl-CpG-binding domain protein 4 (E.C.3.2.2.-)/DNA
Crystal structure of methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
5
N
N
5
N
N
5
N
N
5
N
N
5
N
N
4
N
N
5
N
N
6
N
N
6
N
N
6
N
N
A
SER
107
A
SER
40
HELX_P
A
GLY
119
A
GLY
52
1
1
13
A
LYS
124
A
LYS
57
HELX_P
A
PHE
128
A
PHE
61
5
2
5
disulf
2.043
A
CYS
75
A
SG
CYS
8
1_555
A
CYS
75
A
SG
CYS
8
3_555
covale
1.603
B
DC
8
B
O3'
DC
8
1_555
B
5CM
9
B
P
5CM
9
1_555
covale
1.608
B
5CM
9
B
O3'
5CM
9
1_555
B
DG
10
B
P
DG
10
1_555
hydrog
WATSON-CRICK
B
DG
1
B
N1
DG
1
1_555
C
DC
13
C
N3
DC
13
1_555
hydrog
WATSON-CRICK
B
DG
1
B
N2
DG
1
1_555
C
DC
13
C
O2
DC
13
1_555
hydrog
WATSON-CRICK
B
DG
1
B
O6
DG
1
1_555
C
DC
13
C
N4
DC
13
1_555
hydrog
WATSON-CRICK
B
DT
2
B
N3
DT
2
1_555
C
DA
12
C
N1
DA
12
1_555
hydrog
WATSON-CRICK
B
DT
2
B
O4
DT
2
1_555
C
DA
12
C
N6
DA
12
1_555
hydrog
WATSON-CRICK
B
DC
3
B
N3
DC
3
1_555
C
DG
11
C
N1
DG
11
1_555
hydrog
WATSON-CRICK
B
DC
3
B
N4
DC
3
1_555
C
DG
11
C
O6
DG
11
1_555
hydrog
WATSON-CRICK
B
DC
3
B
O2
DC
3
1_555
C
DG
11
C
N2
DG
11
1_555
hydrog
WATSON-CRICK
B
DA
4
B
N1
DA
4
1_555
C
DT
10
C
N3
DT
10
1_555
hydrog
WATSON-CRICK
B
DA
4
B
N6
DA
4
1_555
C
DT
10
C
O4
DT
10
1_555
hydrog
WATSON-CRICK
B
DC
5
B
N3
DC
5
1_555
C
DG
9
C
N1
DG
9
1_555
hydrog
WATSON-CRICK
B
DC
5
B
N4
DC
5
1_555
C
DG
9
C
O6
DG
9
1_555
hydrog
WATSON-CRICK
B
DC
5
B
O2
DC
5
1_555
C
DG
9
C
N2
DG
9
1_555
hydrog
WATSON-CRICK
B
DT
6
B
N3
DT
6
1_555
C
DA
8
C
N1
DA
8
1_555
hydrog
WATSON-CRICK
B
DT
6
B
O4
DT
6
1_555
C
DA
8
C
N6
DA
8
1_555
hydrog
WATSON-CRICK
B
DA
7
B
N1
DA
7
1_555
C
DT
7
C
N3
DT
7
1_555
hydrog
WATSON-CRICK
B
DA
7
B
N6
DA
7
1_555
C
DT
7
C
O4
DT
7
1_555
hydrog
WATSON-CRICK
B
DC
8
B
N3
DC
8
1_555
C
DG
6
C
N1
DG
6
1_555
hydrog
WATSON-CRICK
B
DC
8
B
N4
DC
8
1_555
C
DG
6
C
O6
DG
6
1_555
hydrog
WATSON-CRICK
B
DC
8
B
O2
DC
8
1_555
C
DG
6
C
N2
DG
6
1_555
hydrog
WATSON-CRICK
B
5CM
9
B
N3
5CM
9
1_555
C
DG
5
C
N1
DG
5
1_555
hydrog
WATSON-CRICK
B
5CM
9
B
N4
5CM
9
1_555
C
DG
5
C
O6
DG
5
1_555
hydrog
WATSON-CRICK
B
5CM
9
B
O2
5CM
9
1_555
C
DG
5
C
N2
DG
5
1_555
hydrog
TYPE_28_PAIR
B
DG
10
B
N1
DG
10
1_555
C
DT
4
C
O2
DT
4
1_555
hydrog
TYPE_28_PAIR
B
DG
10
B
O6
DG
10
1_555
C
DT
4
C
N3
DT
4
1_555
hydrog
WATSON-CRICK
B
DG
11
B
N1
DG
11
1_555
C
DC
3
C
N3
DC
3
1_555
hydrog
WATSON-CRICK
B
DG
11
B
N2
DG
11
1_555
C
DC
3
C
O2
DC
3
1_555
hydrog
WATSON-CRICK
B
DG
11
B
O6
DG
11
1_555
C
DC
3
C
N4
DC
3
1_555
hydrog
WATSON-CRICK
B
DA
12
B
N1
DA
12
1_555
C
DT
2
C
N3
DT
2
1_555
hydrog
WATSON-CRICK
B
DA
12
B
N6
DA
12
1_555
C
DT
2
C
O4
DT
2
1_555
hydrog
WATSON-CRICK
B
DC
13
B
N3
DC
13
1_555
C
DG
1
C
N1
DG
1
1_555
hydrog
WATSON-CRICK
B
DC
13
B
N4
DC
13
1_555
C
DG
1
C
O6
DG
1
1_555
hydrog
WATSON-CRICK
B
DC
13
B
O2
DC
13
1_555
C
DG
1
C
N2
DG
1
1_555
HYDROLASE/DNA
methyl CpG binding domain, protein-DNA complex, versatile base recognition, HYDROLASE-DNA complex
MBD4_MOUSE
UNP
1
69
Q9Z2D7
GHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG
3VXV
PDB
2
3VXV
3VXV
PDB
3
3VXV
69
136
3VXV
69
136
Q9Z2D7
A
1
2
69
1
14
3VXV
1
14
3VXV
B
2
1
14
1
14
3VXV
1
14
3VXV
C
3
1
14
1
EXPRESSION TAG
SER
68
3VXV
A
Q9Z2D7
UNP
1
3
anti-parallel
anti-parallel
A
GLU
78
A
GLU
11
A
GLN
83
A
GLN
16
A
PHE
93
A
PHE
26
A
ILE
98
A
ILE
31
A
LYS
104
A
LYS
37
A
PHE
105
A
PHE
38
BINDING SITE FOR RESIDUE ACT A 201
Software
4
BINDING SITE FOR RESIDUE ACT A 202
Software
3
BINDING SITE FOR RESIDUE EDO A 203
Software
5
BINDING SITE FOR RESIDUE EDO A 204
Software
5
BINDING SITE FOR RESIDUE EDO A 205
Software
4
BINDING SITE FOR RESIDUE EDO A 206
Software
3
BINDING SITE FOR RESIDUE EDO A 207
Software
3
BINDING SITE FOR RESIDUE ACT B 101
Software
4
BINDING SITE FOR RESIDUE EDO C 101
Software
3
A
GLU
120
A
GLU
53
4
1_555
C
DC
13
C
DC
13
4
8_545
C
DT
14
C
DT
14
4
6_445
C
DT
14
C
DT
14
4
8_545
A
GLN
101
A
GLN
34
3
1_555
A
ASN
118
A
ASN
51
3
1_555
A
GLU
120
A
GLU
53
3
1_555
A
GLN
83
A
GLN
16
5
1_555
A
ARG
84
A
ARG
17
5
1_555
A
HOH
318
M
HOH
5
1_555
C
DC
3
C
DC
3
5
1_555
C
DT
4
C
DT
4
5
1_555
A
GLY
76
A
GLY
9
5
1_555
A
GLU
78
A
GLU
11
5
1_555
A
ILE
98
A
ILE
31
5
1_555
A
SER
99
A
SER
32
5
1_555
B
DA
14
B
DA
14
5
2_555
A
CYS
75
A
CYS
8
4
1_555
A
CYS
75
A
CYS
8
4
3_555
A
GLY
76
A
GLY
9
4
1_555
A
TRP
77
A
TRP
10
4
1_555
A
LYS
104
A
LYS
37
3
1_555
A
PHE
105
A
PHE
38
3
1_555
B
ACT
101
K
ACT
3
1_555
A
VAL
132
A
VAL
65
3
1_555
A
LEU
133
A
LEU
66
3
1_555
A
PRO
134
A
PRO
67
3
1_555
A
EDO
206
I
EDO
4
1_555
B
5CM
9
B
5CM
9
4
1_555
B
DG
10
B
DG
10
4
1_555
B
HOH
248
N
HOH
4
1_555
B
DC
13
B
DC
13
3
1_555
C
DT
2
C
DT
2
3
1_555
C
DC
3
C
DC
3
3
1_555
20
C 2 2 21