1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Nagashima, T.
Hayashi, F.
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
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 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
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 Death domain of Nuclear factor NF-kappa-B p100
10.2210/pdb2d96/pdb
pdb_00002d96
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
11223.271
Nuclear factor NF-kappa-B p100 subunit
death domain
1
man
polymer
no
no
GSSGSSGPGLSLGDTALQNLEQLLDGPEAQGSWAELAERLGLRSLVDTYRQTTSPSGSLLRSYELAGGDLAGLLEALSDM
GLEEGVRLLRGPETRDKLPSTEVSGPSSG
GSSGSSGPGLSLGDTALQNLEQLLDGPEAQGSWAELAERLGLRSLVDTYRQTTSPSGSLLRSYELAGGDLAGLLEALSDM
GLEEGVRLLRGPETRDKLPSTEVSGPSSG
A
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
human
Homo
sample
Cell-free protein synthesis
NFKB2
9606
Homo sapiens
plasmid
P050404-15
RIKEN Structural Genomics/Proteomics Initiative
RSGI
NPPSFA, National Project on Protein Structural and Functional Analyses
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2006-12-08
1
1
2008-04-30
1
2
2011-07-13
1
3
2022-03-09
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_ref_seq_dif.details
Y
PDBJ
Y
PDBJ
2005-12-08
REL
REL
target function, structures with the lowest energy
100
20
3D_13C-separated_NOESY
3D_15N-separated_NOESY
120mM
7.0
ambient
298
K
torsion angle dynamics
1
lowest energy
1.15mM death domain U-15N, 13C, 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3
90% H2O/10% D2O
Varian
collection
VNMR
6.1C
Delaglio, F.
processing
NMRPipe
20020425
Johnson, B.A.
data analysis
NMRView
5.0.4
Kobayashi, N.
data analysis
KUJIRA
0.901
Guntert, P.
structure solution
CYANA
2.0.17
Guntert, P.
refinement
CYANA
2.0.17
900
Varian
INOVA
800
Varian
INOVA
GLY
1
n
1
GLY
1
A
SER
2
n
2
SER
2
A
SER
3
n
3
SER
3
A
GLY
4
n
4
GLY
4
A
SER
5
n
5
SER
5
A
SER
6
n
6
SER
6
A
GLY
7
n
7
GLY
7
A
PRO
8
n
8
PRO
8
A
GLY
9
n
9
GLY
9
A
LEU
10
n
10
LEU
10
A
SER
11
n
11
SER
11
A
LEU
12
n
12
LEU
12
A
GLY
13
n
13
GLY
13
A
ASP
14
n
14
ASP
14
A
THR
15
n
15
THR
15
A
ALA
16
n
16
ALA
16
A
LEU
17
n
17
LEU
17
A
GLN
18
n
18
GLN
18
A
ASN
19
n
19
ASN
19
A
LEU
20
n
20
LEU
20
A
GLU
21
n
21
GLU
21
A
GLN
22
n
22
GLN
22
A
LEU
23
n
23
LEU
23
A
LEU
24
n
24
LEU
24
A
ASP
25
n
25
ASP
25
A
GLY
26
n
26
GLY
26
A
PRO
27
n
27
PRO
27
A
GLU
28
n
28
GLU
28
A
ALA
29
n
29
ALA
29
A
GLN
30
n
30
GLN
30
A
GLY
31
n
31
GLY
31
A
SER
32
n
32
SER
32
A
TRP
33
n
33
TRP
33
A
ALA
34
n
34
ALA
34
A
GLU
35
n
35
GLU
35
A
LEU
36
n
36
LEU
36
A
ALA
37
n
37
ALA
37
A
GLU
38
n
38
GLU
38
A
ARG
39
n
39
ARG
39
A
LEU
40
n
40
LEU
40
A
GLY
41
n
41
GLY
41
A
LEU
42
n
42
LEU
42
A
ARG
43
n
43
ARG
43
A
SER
44
n
44
SER
44
A
LEU
45
n
45
LEU
45
A
VAL
46
n
46
VAL
46
A
ASP
47
n
47
ASP
47
A
THR
48
n
48
THR
48
A
TYR
49
n
49
TYR
49
A
ARG
50
n
50
ARG
50
A
GLN
51
n
51
GLN
51
A
THR
52
n
52
THR
52
A
THR
53
n
53
THR
53
A
SER
54
n
54
SER
54
A
PRO
55
n
55
PRO
55
A
SER
56
n
56
SER
56
A
GLY
57
n
57
GLY
57
A
SER
58
n
58
SER
58
A
LEU
59
n
59
LEU
59
A
LEU
60
n
60
LEU
60
A
ARG
61
n
61
ARG
61
A
SER
62
n
62
SER
62
A
TYR
63
n
63
TYR
63
A
GLU
64
n
64
GLU
64
A
LEU
65
n
65
LEU
65
A
ALA
66
n
66
ALA
66
A
GLY
67
n
67
GLY
67
A
GLY
68
n
68
GLY
68
A
ASP
69
n
69
ASP
69
A
LEU
70
n
70
LEU
70
A
ALA
71
n
71
ALA
71
A
GLY
72
n
72
GLY
72
A
LEU
73
n
73
LEU
73
A
LEU
74
n
74
LEU
74
A
GLU
75
n
75
GLU
75
A
ALA
76
n
76
ALA
76
A
LEU
77
n
77
LEU
77
A
SER
78
n
78
SER
78
A
ASP
79
n
79
ASP
79
A
MET
80
n
80
MET
80
A
GLY
81
n
81
GLY
81
A
LEU
82
n
82
LEU
82
A
GLU
83
n
83
GLU
83
A
GLU
84
n
84
GLU
84
A
GLY
85
n
85
GLY
85
A
VAL
86
n
86
VAL
86
A
ARG
87
n
87
ARG
87
A
LEU
88
n
88
LEU
88
A
LEU
89
n
89
LEU
89
A
ARG
90
n
90
ARG
90
A
GLY
91
n
91
GLY
91
A
PRO
92
n
92
PRO
92
A
GLU
93
n
93
GLU
93
A
THR
94
n
94
THR
94
A
ARG
95
n
95
ARG
95
A
ASP
96
n
96
ASP
96
A
LYS
97
n
97
LYS
97
A
LEU
98
n
98
LEU
98
A
PRO
99
n
99
PRO
99
A
SER
100
n
100
SER
100
A
THR
101
n
101
THR
101
A
GLU
102
n
102
GLU
102
A
VAL
103
n
103
VAL
103
A
SER
104
n
104
SER
104
A
GLY
105
n
105
GLY
105
A
PRO
106
n
106
PRO
106
A
SER
107
n
107
SER
107
A
SER
108
n
108
SER
108
A
GLY
109
n
109
GLY
109
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
ALA
29
-48.49
100.77
1
A
LEU
42
-95.10
36.76
1
A
SER
54
-119.50
71.35
1
A
LEU
82
-58.90
91.13
1
A
SER
108
72.63
41.50
2
A
SER
5
-123.67
-61.44
2
A
SER
6
-66.76
85.64
2
A
PRO
8
-69.81
1.71
2
A
ALA
29
-48.62
99.69
2
A
GLN
30
-39.80
-32.73
2
A
VAL
46
-39.09
-25.72
2
A
THR
48
-36.63
-34.79
2
A
SER
54
-114.66
63.02
2
A
SER
56
-93.64
-69.27
2
A
LEU
77
-37.94
-39.09
2
A
LEU
82
-69.07
71.26
2
A
PRO
99
-69.77
84.49
2
A
SER
107
37.85
42.61
3
A
SER
5
-91.37
45.84
3
A
ALA
29
-41.63
102.91
3
A
LEU
42
-95.59
40.11
3
A
LEU
82
-53.37
94.39
3
A
PRO
92
-69.74
-179.07
3
A
ARG
95
-35.80
135.12
4
A
SER
11
-79.72
46.10
4
A
ALA
29
-40.87
103.71
4
A
GLN
30
-39.94
-33.29
4
A
LEU
42
-91.71
54.00
5
A
SER
6
-49.13
169.79
5
A
ALA
29
-33.99
112.60
5
A
GLN
30
-78.86
44.99
5
A
VAL
46
-47.28
-19.90
5
A
SER
54
-115.06
77.58
6
A
PRO
8
-69.75
1.84
6
A
LEU
12
-46.33
157.14
6
A
ALA
29
-34.21
111.17
6
A
LEU
42
-111.08
53.28
6
A
SER
54
-119.11
79.60
6
A
LEU
98
-38.78
139.33
6
A
PRO
99
-69.76
97.48
7
A
SER
5
-37.83
148.44
7
A
LEU
10
-37.55
131.08
7
A
ALA
29
-52.31
97.70
7
A
LEU
42
-114.16
50.05
7
A
THR
52
-62.14
-178.07
7
A
SER
54
-115.27
77.44
7
A
LEU
82
-49.31
94.12
7
A
PRO
92
-69.76
-167.29
7
A
ARG
95
35.04
42.57
7
A
THR
101
-162.29
114.42
8
A
SER
2
-49.60
98.72
8
A
ALA
29
-50.72
105.39
8
A
PRO
99
-69.78
87.99
8
A
SER
104
-36.95
130.10
8
A
PRO
106
-69.75
-174.23
9
A
SER
3
-55.78
102.85
9
A
ALA
29
-52.21
101.92
9
A
SER
32
-173.53
-179.67
9
A
GLU
93
-81.75
43.10
9
A
LYS
97
-172.15
141.47
10
A
ASP
14
-38.55
-39.79
10
A
ALA
29
-34.92
111.21
10
A
LEU
42
-105.79
45.36
10
A
SER
54
-111.53
69.76
10
A
SER
100
-56.88
104.53
11
A
ALA
29
-40.85
99.24
11
A
LYS
97
-173.68
146.52
11
A
SER
107
38.25
51.06
12
A
ALA
29
-40.70
103.20
12
A
LEU
42
-98.11
49.65
12
A
SER
54
-116.33
79.34
12
A
ASP
96
-37.36
149.65
12
A
SER
100
-39.96
119.50
12
A
SER
107
-123.06
-52.01
13
A
SER
3
-36.78
137.71
13
A
ALA
29
-44.06
109.06
13
A
THR
52
-54.65
177.11
13
A
LEU
82
-58.72
93.04
13
A
PRO
92
-69.77
-172.97
14
A
ALA
29
-48.13
108.46
14
A
LEU
42
-99.21
54.82
14
A
THR
52
-47.71
158.41
14
A
SER
54
-119.97
75.96
14
A
PRO
106
-69.81
-174.54
14
A
SER
108
-84.38
36.36
15
A
SER
5
38.13
40.99
15
A
GLN
18
-38.31
-35.01
15
A
ALA
29
-54.86
94.65
15
A
LEU
42
-111.26
50.13
15
A
THR
52
-52.64
-179.31
15
A
SER
54
-116.26
77.15
15
A
PRO
55
-69.79
1.99
15
A
ASP
96
-38.52
122.91
15
A
LEU
98
-35.42
140.76
15
A
VAL
103
-36.12
151.63
16
A
SER
11
-76.93
47.85
16
A
ALA
29
-34.01
112.46
16
A
GLN
30
-80.85
41.83
16
A
LEU
42
-100.69
40.83
16
A
GLN
51
-58.68
-70.10
16
A
THR
52
-53.25
174.45
16
A
SER
54
-109.43
71.84
16
A
LEU
82
-48.90
93.64
16
A
PRO
99
-69.73
98.34
17
A
SER
2
-37.98
134.94
17
A
SER
11
-36.70
-31.48
17
A
LEU
12
-46.38
157.17
17
A
ALA
29
-33.74
114.02
17
A
GLN
30
-82.56
38.17
17
A
LEU
42
-101.10
46.13
17
A
SER
56
-39.73
-34.96
17
A
LEU
82
-53.82
85.01
17
A
VAL
103
-98.33
-61.51
18
A
PRO
8
-69.71
0.31
18
A
SER
11
-84.07
35.05
18
A
ALA
29
-49.50
99.18
18
A
LEU
82
-51.07
95.88
18
A
PRO
92
-69.76
-173.69
18
A
LEU
98
-36.87
153.73
18
A
SER
104
-161.67
112.33
18
A
SER
107
-39.65
108.10
19
A
SER
5
-58.08
-175.06
19
A
ALA
29
-52.52
85.03
19
A
GLN
30
-33.90
-36.72
19
A
LEU
82
-46.64
89.79
19
A
LYS
97
35.84
39.76
19
A
SER
107
-39.92
149.38
20
A
ALA
29
-64.71
95.96
20
A
LEU
42
-103.05
51.71
20
A
GLN
51
-39.27
-73.18
20
A
SER
54
-115.60
78.29
20
A
SER
56
-40.07
-71.79
20
A
LEU
82
-56.47
87.16
20
A
PRO
99
-69.76
97.13
Solution structure of the Death domain of Nuclear factor NF-kappa-B p100
1
N
N
A
GLY
13
A
GLY
13
HELX_P
A
ASP
25
A
ASP
25
1
1
13
A
SER
32
A
SER
32
HELX_P
A
GLY
41
A
GLY
41
1
2
10
A
LEU
42
A
LEU
42
HELX_P
A
GLN
51
A
GLN
51
1
3
10
A
SER
54
A
SER
54
HELX_P
A
ALA
66
A
ALA
66
1
4
13
A
ASP
69
A
ASP
69
HELX_P
A
GLY
81
A
GLY
81
1
5
13
A
LEU
82
A
LEU
82
HELX_P
A
GLY
91
A
GLY
91
1
6
10
TRANSCRIPTION
six helix bundle, processing, proteasome, signal transduction, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, TRANSCRIPTION
NFKB2_HUMAN
UNP
1
766
Q00653
PGLSLGDTALQNLEQLLDGPEAQGSWAELAERLGLRSLVDTYRQTTSPSGSLLRSYELAGGDLAGLLEALSDMGLEEGVR
LLRGPETRDKLPSTEV
766
861
2D96
8
103
Q00653
A
1
8
103
1
cloning artifact
GLY
1
2D96
A
Q00653
UNP
1
1
cloning artifact
SER
2
2D96
A
Q00653
UNP
2
1
cloning artifact
SER
3
2D96
A
Q00653
UNP
3
1
cloning artifact
GLY
4
2D96
A
Q00653
UNP
4
1
cloning artifact
SER
5
2D96
A
Q00653
UNP
5
1
cloning artifact
SER
6
2D96
A
Q00653
UNP
6
1
cloning artifact
GLY
7
2D96
A
Q00653
UNP
7
1
cloning artifact
SER
104
2D96
A
Q00653
UNP
104
1
cloning artifact
GLY
105
2D96
A
Q00653
UNP
105
1
cloning artifact
PRO
106
2D96
A
Q00653
UNP
106
1
cloning artifact
SER
107
2D96
A
Q00653
UNP
107
1
cloning artifact
SER
108
2D96
A
Q00653
UNP
108
1
cloning artifact
GLY
109
2D96
A
Q00653
UNP
109