1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Tanabe, W.
Suzuki, S.
Muto, Y.
Inoue, M.
Kigawa, T.
Terada, T.
Shirouzu, M.
Yokoyama, S.
RIKEN Structural Genomics/Proteomics Initiative (RSGI)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
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
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
To be Published
0353
Solution structure of the ARID domain of Jarid1b protein
10.2210/pdb2eqy/pdb
pdb_00002eqy
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
13720.741
Jumonji, AT rich interactive domain 1B
ARID domain
1
man
polymer
Rbp2 like
no
no
GSSGSSGEAQTRVKLNFLDQIAKYWELQGSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKA
VGSHIRGHYERILNPYNLFLSGDSLRCLQKPNLTSDTKDKEY
GSSGSSGEAQTRVKLNFLDQIAKYWELQGSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKA
VGSHIRGHYERILNPYNLFLSGDSLRCLQKPNLTSDTKDKEY
A
mmt007003997.1
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
house mouse
Mus
sample
Cell-free protein synthesis
Jarid1b
10090
Mus musculus
Plasmid
P060821-07
RIKEN Structural Genomics/Proteomics Initiative
RSGI
NPPSFA, National Project on Protein Structural and Functional Analyses
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
repository
Initial release
Version format compliance
Data collection
Database references
Derived calculations
1
0
2007-10-02
1
1
2011-07-13
1
2
2022-03-09
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_ref_seq_dif.details
Y
PDBJ
Y
PDBJ
2007-03-30
REL
REL
structures with the least restraint violations, structures with the lowest energy, target function
100
20
3D_15N-separated_NOESY
3D_13C-separated_NOESY
120mM
7.0
ambient
298
K
torsion angle dyanamics, simulated annealing
1
lowest energy
0.77mM 13C-15N PROTEIN; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
90% H2O/10% D2O
Bruker
collection
XwinNMR
3.5
Delaglio, F.
processing
NMRPipe
20060702
Johnson, B.A.
data analysis
NMRView
5.0.4
Kobayashi, N.
data analysis
KUJIRA
0.9820
Guntert, P.
structure solution
CYANA
2.0.17
Guntert, P.
refinement
CYANA
2.0.17
800
Bruker
AVANCE
GLY
87
n
1
GLY
87
A
SER
88
n
2
SER
88
A
SER
89
n
3
SER
89
A
GLY
90
n
4
GLY
90
A
SER
91
n
5
SER
91
A
SER
92
n
6
SER
92
A
GLY
93
n
7
GLY
93
A
GLU
94
n
8
GLU
94
A
ALA
95
n
9
ALA
95
A
GLN
96
n
10
GLN
96
A
THR
97
n
11
THR
97
A
ARG
98
n
12
ARG
98
A
VAL
99
n
13
VAL
99
A
LYS
100
n
14
LYS
100
A
LEU
101
n
15
LEU
101
A
ASN
102
n
16
ASN
102
A
PHE
103
n
17
PHE
103
A
LEU
104
n
18
LEU
104
A
ASP
105
n
19
ASP
105
A
GLN
106
n
20
GLN
106
A
ILE
107
n
21
ILE
107
A
ALA
108
n
22
ALA
108
A
LYS
109
n
23
LYS
109
A
TYR
110
n
24
TYR
110
A
TRP
111
n
25
TRP
111
A
GLU
112
n
26
GLU
112
A
LEU
113
n
27
LEU
113
A
GLN
114
n
28
GLN
114
A
GLY
115
n
29
GLY
115
A
SER
116
n
30
SER
116
A
THR
117
n
31
THR
117
A
LEU
118
n
32
LEU
118
A
LYS
119
n
33
LYS
119
A
ILE
120
n
34
ILE
120
A
PRO
121
n
35
PRO
121
A
HIS
122
n
36
HIS
122
A
VAL
123
n
37
VAL
123
A
GLU
124
n
38
GLU
124
A
ARG
125
n
39
ARG
125
A
LYS
126
n
40
LYS
126
A
ILE
127
n
41
ILE
127
A
LEU
128
n
42
LEU
128
A
ASP
129
n
43
ASP
129
A
LEU
130
n
44
LEU
130
A
PHE
131
n
45
PHE
131
A
GLN
132
n
46
GLN
132
A
LEU
133
n
47
LEU
133
A
ASN
134
n
48
ASN
134
A
LYS
135
n
49
LYS
135
A
LEU
136
n
50
LEU
136
A
VAL
137
n
51
VAL
137
A
ALA
138
n
52
ALA
138
A
GLU
139
n
53
GLU
139
A
GLU
140
n
54
GLU
140
A
GLY
141
n
55
GLY
141
A
GLY
142
n
56
GLY
142
A
PHE
143
n
57
PHE
143
A
ALA
144
n
58
ALA
144
A
VAL
145
n
59
VAL
145
A
VAL
146
n
60
VAL
146
A
CYS
147
n
61
CYS
147
A
LYS
148
n
62
LYS
148
A
ASP
149
n
63
ASP
149
A
ARG
150
n
64
ARG
150
A
LYS
151
n
65
LYS
151
A
TRP
152
n
66
TRP
152
A
THR
153
n
67
THR
153
A
LYS
154
n
68
LYS
154
A
ILE
155
n
69
ILE
155
A
ALA
156
n
70
ALA
156
A
THR
157
n
71
THR
157
A
LYS
158
n
72
LYS
158
A
MET
159
n
73
MET
159
A
GLY
160
n
74
GLY
160
A
PHE
161
n
75
PHE
161
A
ALA
162
n
76
ALA
162
A
PRO
163
n
77
PRO
163
A
GLY
164
n
78
GLY
164
A
LYS
165
n
79
LYS
165
A
ALA
166
n
80
ALA
166
A
VAL
167
n
81
VAL
167
A
GLY
168
n
82
GLY
168
A
SER
169
n
83
SER
169
A
HIS
170
n
84
HIS
170
A
ILE
171
n
85
ILE
171
A
ARG
172
n
86
ARG
172
A
GLY
173
n
87
GLY
173
A
HIS
174
n
88
HIS
174
A
TYR
175
n
89
TYR
175
A
GLU
176
n
90
GLU
176
A
ARG
177
n
91
ARG
177
A
ILE
178
n
92
ILE
178
A
LEU
179
n
93
LEU
179
A
ASN
180
n
94
ASN
180
A
PRO
181
n
95
PRO
181
A
TYR
182
n
96
TYR
182
A
ASN
183
n
97
ASN
183
A
LEU
184
n
98
LEU
184
A
PHE
185
n
99
PHE
185
A
LEU
186
n
100
LEU
186
A
SER
187
n
101
SER
187
A
GLY
188
n
102
GLY
188
A
ASP
189
n
103
ASP
189
A
SER
190
n
104
SER
190
A
LEU
191
n
105
LEU
191
A
ARG
192
n
106
ARG
192
A
CYS
193
n
107
CYS
193
A
LEU
194
n
108
LEU
194
A
GLN
195
n
109
GLN
195
A
LYS
196
n
110
LYS
196
A
PRO
197
n
111
PRO
197
A
ASN
198
n
112
ASN
198
A
LEU
199
n
113
LEU
199
A
THR
200
n
114
THR
200
A
SER
201
n
115
SER
201
A
ASP
202
n
116
ASP
202
A
THR
203
n
117
THR
203
A
LYS
204
n
118
LYS
204
A
ASP
205
n
119
ASP
205
A
LYS
206
n
120
LYS
206
A
GLU
207
n
121
GLU
207
A
TYR
208
n
122
TYR
208
A
author_defined_assembly
1
monomeric
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
1
A
SER
92
-171.35
144.75
1
A
GLN
96
-128.96
-58.32
1
A
LEU
133
-34.09
-71.92
1
A
ARG
150
35.36
51.48
1
A
LYS
151
-86.47
41.91
1
A
ILE
155
-55.23
-70.90
1
A
PRO
163
-69.75
85.64
1
A
LYS
165
-131.44
-46.26
1
A
ASP
189
-59.15
101.68
1
A
ARG
192
-45.20
101.40
1
A
PRO
197
-69.74
-179.69
1
A
LEU
199
-34.39
142.25
2
A
SER
88
-48.33
160.03
2
A
SER
92
-134.14
-51.42
2
A
ARG
150
38.38
39.12
2
A
LYS
151
-85.46
46.60
2
A
PRO
163
-69.73
96.19
2
A
ARG
192
-61.28
92.53
2
A
LYS
206
-36.34
141.39
3
A
GLU
94
-96.17
34.50
3
A
LEU
104
-38.23
-27.88
3
A
LEU
133
-36.45
-70.16
3
A
ARG
150
39.64
52.12
3
A
LYS
151
-94.22
42.13
3
A
PRO
163
-69.80
88.32
4
A
THR
97
-34.16
-36.01
4
A
LEU
133
-50.08
-71.76
4
A
ARG
150
31.41
47.87
4
A
LYS
151
-87.97
37.95
4
A
PRO
163
-69.75
93.32
5
A
SER
88
-170.34
145.14
5
A
SER
92
-37.06
120.46
5
A
LEU
104
-36.68
-30.61
5
A
LEU
133
-46.94
-70.83
5
A
ILE
178
-120.13
-50.35
5
A
GLU
207
-66.37
96.45
6
A
SER
88
37.85
41.60
6
A
LYS
126
-170.25
133.19
6
A
LEU
133
-40.79
-70.69
6
A
LYS
151
-83.53
43.11
7
A
GLN
96
-81.13
46.14
7
A
GLU
124
37.79
42.00
7
A
LEU
128
-67.31
94.83
7
A
LEU
133
-37.93
-72.13
7
A
ARG
150
34.38
37.91
7
A
LYS
151
-79.74
44.03
7
A
PRO
163
-69.79
86.70
7
A
ASP
189
-88.97
46.18
7
A
ARG
192
-36.91
113.20
7
A
LEU
194
-52.68
98.79
8
A
ILE
127
-60.68
99.14
8
A
LEU
133
-47.91
-72.12
8
A
SER
190
-97.97
-61.58
8
A
SER
201
-49.33
165.83
8
A
GLU
207
-58.27
-178.91
9
A
LEU
133
-43.93
-71.48
9
A
LYS
151
-96.16
36.29
9
A
CYS
193
-43.40
91.08
9
A
ASN
198
-53.39
95.64
10
A
ALA
95
-107.13
40.77
10
A
LEU
133
-35.47
-71.97
10
A
ARG
150
34.49
41.32
10
A
LYS
151
-86.07
40.59
10
A
PRO
163
-69.77
85.73
10
A
ILE
178
-120.36
-51.90
10
A
GLN
195
-46.40
173.32
11
A
SER
88
-38.93
109.73
11
A
SER
92
-50.89
173.94
11
A
THR
97
-33.79
-34.59
11
A
PRO
121
-69.81
-177.21
11
A
ASP
129
-56.22
103.28
11
A
LEU
133
-38.15
-72.08
11
A
LYS
151
-81.92
40.56
11
A
ILE
155
-51.80
-72.59
11
A
PRO
163
-69.74
84.42
11
A
LEU
179
-92.84
35.68
11
A
ARG
192
-35.30
117.00
11
A
LYS
196
-37.37
141.34
11
A
PRO
197
-69.77
-177.34
11
A
GLU
207
-37.22
114.30
12
A
LEU
104
-39.72
-39.52
12
A
TYR
110
-38.54
-26.24
12
A
GLU
112
-49.61
-18.41
12
A
PRO
121
-69.81
-179.29
12
A
ASP
129
-62.70
83.73
12
A
LEU
133
-35.68
-71.58
12
A
ARG
150
37.62
48.91
12
A
LYS
151
-86.87
40.70
12
A
PRO
163
-69.76
86.20
12
A
ILE
178
-120.10
-51.40
12
A
LEU
184
-39.06
-27.11
12
A
ASP
189
-47.01
109.97
12
A
ASN
198
-48.27
159.40
13
A
LEU
133
-50.65
-71.17
13
A
LYS
151
-83.42
36.74
13
A
PRO
163
-69.76
85.03
13
A
LYS
204
-39.35
114.64
13
A
ASP
205
-48.63
163.24
14
A
SER
92
-44.69
109.66
14
A
VAL
146
-65.03
-70.56
14
A
LYS
151
-98.25
41.13
14
A
PRO
163
-69.76
94.78
14
A
ILE
178
-120.11
-52.39
14
A
ASP
202
-54.82
107.71
15
A
LEU
104
-38.40
-32.01
15
A
LEU
133
-44.43
-71.79
15
A
ARG
150
35.72
52.29
15
A
PRO
163
-69.73
85.20
15
A
ILE
178
-120.09
-51.73
15
A
PRO
197
-69.79
-171.20
15
A
GLU
207
-56.13
-178.69
16
A
TYR
110
-38.79
-25.84
16
A
LEU
128
-66.80
93.89
16
A
LEU
133
-49.63
-72.12
16
A
PRO
163
-69.70
88.46
16
A
ARG
192
-69.01
96.13
16
A
CYS
193
-40.22
154.99
16
A
LEU
194
-38.74
119.37
16
A
LYS
196
-43.89
156.09
16
A
PRO
197
-69.76
86.72
16
A
LEU
199
-65.51
76.32
16
A
SER
201
-68.19
78.67
17
A
GLU
94
-106.97
41.29
17
A
THR
97
-92.20
-67.87
17
A
GLU
112
-38.31
-36.01
17
A
ARG
150
35.02
45.17
17
A
LYS
151
-93.36
47.92
17
A
ILE
178
-120.01
-51.39
17
A
LEU
199
-36.31
119.61
18
A
GLU
94
-86.96
39.09
18
A
LEU
104
-37.03
-37.58
18
A
LEU
133
-52.66
-71.18
18
A
LYS
151
-89.38
46.79
18
A
PRO
163
-69.80
90.02
18
A
LEU
179
-91.45
33.75
18
A
TYR
182
-37.74
-36.80
18
A
PRO
197
-69.82
89.06
19
A
ARG
150
34.49
38.09
19
A
LYS
151
-76.90
47.56
19
A
ARG
192
-35.91
141.62
19
A
GLN
195
-43.97
105.40
20
A
ALA
95
-125.78
-53.77
20
A
GLN
96
-91.32
45.08
20
A
ARG
150
38.86
48.67
20
A
LYS
151
-84.51
38.49
20
A
PRO
163
-69.73
85.39
20
A
LYS
165
-37.36
-33.52
20
A
ASP
189
-34.44
109.98
Solution structure of the ARID domain of Jarid1b protein
1
N
N
A
GLN
96
A
GLN
10
HELX_P
A
GLY
115
A
GLY
29
1
1
20
A
ASP
129
A
ASP
43
HELX_P
A
GLY
141
A
GLY
55
1
2
13
A
GLY
142
A
GLY
56
HELX_P
A
ASP
149
A
ASP
63
1
3
8
A
LYS
151
A
LYS
65
HELX_P
A
MET
159
A
MET
73
1
4
9
A
LYS
165
A
LYS
79
HELX_P
A
ILE
178
A
ILE
92
1
5
14
A
ILE
178
A
ILE
92
HELX_P
A
GLY
188
A
GLY
102
1
6
11
DNA BINDING PROTEIN
ARID domain, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, DNA BINDING PROTEIN
Q80Y84_MOUSE
UNP
1
94
Q80Y84
EAQTRVKLNFLDQIAKYWELQGSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRG
HYERILNPYNLFLSGDSLRCLQKPNLTSDTKDKEY
94
208
2EQY
94
208
Q80Y84
A
1
8
122
1
expression tag
GLY
87
2EQY
A
Q80Y84
UNP
1
1
expression tag
SER
88
2EQY
A
Q80Y84
UNP
2
1
expression tag
SER
89
2EQY
A
Q80Y84
UNP
3
1
expression tag
GLY
90
2EQY
A
Q80Y84
UNP
4
1
expression tag
SER
91
2EQY
A
Q80Y84
UNP
5
1
expression tag
SER
92
2EQY
A
Q80Y84
UNP
6
1
expression tag
GLY
93
2EQY
A
Q80Y84
UNP
7