1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Miyamoto, K.
Tomizawa, T.
Koshiba, S.
Inoue, M.
Kigawa, T.
Yokoyama, S.
RIKEN Structural Genomics/Proteomics Initiative (RSGI)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
Zn 2
65.409
ZINC ION
non-polymer
To be Published
0353
Solution Structure of the zinc finger BED domain of the zinc finger BED domain containing protein 1
10.2210/pdb2ct5/pdb
pdb_00002ct5
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
8072.971
Zinc finger BED domain containing protein 1
zinc finger BED domain
1
man
polymer
65.409
ZINC ION
1
syn
non-polymer
dREF homolog, Putative Ac-like transposable element
no
no
GSSGSSGSKVWKYFGFDTNAEGCILQWKKIYCRICMAQIAYSGNTSNLSYHLEKNHPEEFCEFVKSNSGPSSG
GSSGSSGSKVWKYFGFDTNAEGCILQWKKIYCRICMAQIAYSGNTSNLSYHLEKNHPEEFCEFVKSNSGPSSG
A
hsk002000767.1
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
human
Homo
sample
Cell-free protein synthesis
ZBED1X
9606
Homo sapiens
PLASMID
P040308-29
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_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2005-11-23
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
_pdbx_nmr_spectrometer.model
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
PDBJ
Y
PDBJ
2005-05-23
REL
ZN
ZINC ION
target function, structures with the least restraint violations
100
20
3D_15N-separated_NOESY
3D_13C-separated_NOESY
120
7.0
ambient
296
K
torsion angle dynamics
1
lowest energy
1.09mM zinc finger BED domain U-13C, 15N; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.01mM ZNCl2; 90% H2O, 10% D2O
90% H2O/10% D2O
Bruker
collection
XwinNMR
2.6
Delaglio, F.
processing
NMRPipe
20031121
Johnson, B. A.
data analysis
NMRView
5.0.4
Kobayashi, N.
data analysis
KUJIRA
0.925
Guntert, P.
structure solution
CYANA
2.0.17
Guntert, P.
refinement
CYANA
2.0.17
800
Bruker
AVANCE
ZN
201
2
ZN
ZN
201
A
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
SER
8
n
8
SER
8
A
LYS
9
n
9
LYS
9
A
VAL
10
n
10
VAL
10
A
TRP
11
n
11
TRP
11
A
LYS
12
n
12
LYS
12
A
TYR
13
n
13
TYR
13
A
PHE
14
n
14
PHE
14
A
GLY
15
n
15
GLY
15
A
PHE
16
n
16
PHE
16
A
ASP
17
n
17
ASP
17
A
THR
18
n
18
THR
18
A
ASN
19
n
19
ASN
19
A
ALA
20
n
20
ALA
20
A
GLU
21
n
21
GLU
21
A
GLY
22
n
22
GLY
22
A
CYS
23
n
23
CYS
23
A
ILE
24
n
24
ILE
24
A
LEU
25
n
25
LEU
25
A
GLN
26
n
26
GLN
26
A
TRP
27
n
27
TRP
27
A
LYS
28
n
28
LYS
28
A
LYS
29
n
29
LYS
29
A
ILE
30
n
30
ILE
30
A
TYR
31
n
31
TYR
31
A
CYS
32
n
32
CYS
32
A
ARG
33
n
33
ARG
33
A
ILE
34
n
34
ILE
34
A
CYS
35
n
35
CYS
35
A
MET
36
n
36
MET
36
A
ALA
37
n
37
ALA
37
A
GLN
38
n
38
GLN
38
A
ILE
39
n
39
ILE
39
A
ALA
40
n
40
ALA
40
A
TYR
41
n
41
TYR
41
A
SER
42
n
42
SER
42
A
GLY
43
n
43
GLY
43
A
ASN
44
n
44
ASN
44
A
THR
45
n
45
THR
45
A
SER
46
n
46
SER
46
A
ASN
47
n
47
ASN
47
A
LEU
48
n
48
LEU
48
A
SER
49
n
49
SER
49
A
TYR
50
n
50
TYR
50
A
HIS
51
n
51
HIS
51
A
LEU
52
n
52
LEU
52
A
GLU
53
n
53
GLU
53
A
LYS
54
n
54
LYS
54
A
ASN
55
n
55
ASN
55
A
HIS
56
n
56
HIS
56
A
PRO
57
n
57
PRO
57
A
GLU
58
n
58
GLU
58
A
GLU
59
n
59
GLU
59
A
PHE
60
n
60
PHE
60
A
CYS
61
n
61
CYS
61
A
GLU
62
n
62
GLU
62
A
PHE
63
n
63
PHE
63
A
VAL
64
n
64
VAL
64
A
LYS
65
n
65
LYS
65
A
SER
66
n
66
SER
66
A
ASN
67
n
67
ASN
67
A
SER
68
n
68
SER
68
A
GLY
69
n
69
GLY
69
A
PRO
70
n
70
PRO
70
A
SER
71
n
71
SER
71
A
SER
72
n
72
SER
72
A
GLY
73
n
73
GLY
73
A
author_defined_assembly
1
monomeric
A
CYS
32
A
SG
CYS
32
1_555
A
ZN
201
B
ZN
ZN
1_555
A
CYS
35
A
SG
CYS
35
1_555
106.9
A
CYS
32
A
SG
CYS
32
1_555
A
ZN
201
B
ZN
ZN
1_555
A
HIS
51
A
NE2
HIS
51
1_555
92.4
A
CYS
35
A
SG
CYS
35
1_555
A
ZN
201
B
ZN
ZN
1_555
A
HIS
51
A
NE2
HIS
51
1_555
117.5
A
CYS
32
A
SG
CYS
32
1_555
A
ZN
201
B
ZN
ZN
1_555
A
HIS
56
A
NE2
HIS
56
1_555
117.9
A
CYS
35
A
SG
CYS
35
1_555
A
ZN
201
B
ZN
ZN
1_555
A
HIS
56
A
NE2
HIS
56
1_555
104.0
A
HIS
51
A
NE2
HIS
51
1_555
A
ZN
201
B
ZN
ZN
1_555
A
HIS
56
A
NE2
HIS
56
1_555
118.1
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
CYS
32
A
N
CYS
32
A
O
ALA
37
A
O
ALA
37
1
A
SER
2
-124.33
-50.31
1
A
VAL
10
-85.80
36.46
1
A
ASP
17
-105.92
79.79
1
A
TRP
27
-59.28
172.45
1
A
MET
36
36.91
44.81
1
A
THR
45
-86.63
38.40
1
A
GLU
53
-38.81
-32.18
1
A
ASN
55
-71.15
-76.39
2
A
SER
5
-82.36
43.61
2
A
LYS
12
-37.57
-37.74
2
A
ASN
19
71.94
36.83
2
A
GLN
26
-82.54
41.06
2
A
ARG
33
-86.06
33.01
2
A
MET
36
34.67
48.15
2
A
ASN
44
-46.56
155.05
2
A
ASN
55
-83.24
-70.50
2
A
VAL
64
-97.54
48.17
2
A
SER
71
-168.35
105.27
3
A
SER
5
-54.68
96.10
3
A
LYS
9
47.59
27.99
3
A
CYS
23
-36.81
152.59
3
A
SER
42
-124.04
-54.61
3
A
ASN
44
38.44
39.53
3
A
THR
45
35.36
52.07
3
A
GLU
53
-49.77
-18.68
3
A
ASN
55
-111.08
-70.91
3
A
LYS
65
-96.44
40.13
3
A
PRO
70
-69.78
-174.61
3
A
SER
72
-39.39
138.90
4
A
SER
3
-65.77
82.00
4
A
TRP
11
-91.63
39.79
4
A
GLN
26
-33.99
141.11
4
A
THR
45
35.07
45.81
4
A
ASN
55
-95.09
-60.39
5
A
SER
5
-64.44
91.02
5
A
TRP
11
-94.13
34.06
5
A
ASP
17
-55.01
-73.99
5
A
ASN
19
-35.27
102.74
5
A
GLU
21
-66.44
78.15
5
A
CYS
23
-41.64
152.13
5
A
ILE
24
-35.34
144.98
5
A
LYS
28
-174.98
115.48
5
A
MET
36
35.51
45.01
5
A
THR
45
37.08
42.20
5
A
ASN
55
-93.67
-73.88
5
A
ASN
67
-34.99
108.21
5
A
SER
72
70.98
42.12
6
A
LYS
12
-34.37
-39.13
6
A
ASP
17
-63.91
94.61
6
A
ILE
24
-35.41
139.83
6
A
LEU
25
-133.09
-34.43
6
A
MET
36
39.11
53.63
6
A
THR
45
-94.12
48.12
6
A
ASN
55
-109.65
-67.95
6
A
SER
68
-36.03
151.92
7
A
GLN
26
-46.28
173.58
7
A
MET
36
37.56
39.64
7
A
ASN
44
-109.25
79.74
7
A
THR
45
35.68
45.00
7
A
ASN
55
-101.52
-66.32
7
A
SER
68
-52.65
172.40
7
A
PRO
70
-69.79
86.30
8
A
SER
6
37.76
40.45
8
A
LYS
9
-80.85
42.07
8
A
ASP
17
-60.98
-71.86
8
A
THR
18
38.35
44.02
8
A
ASN
19
-43.94
100.93
8
A
LEU
25
-106.91
41.22
8
A
GLN
26
-171.02
149.73
8
A
TRP
27
-35.00
140.40
8
A
LYS
28
-69.61
94.56
8
A
MET
36
38.32
39.04
8
A
THR
45
-86.21
45.54
8
A
ASN
55
-108.94
-60.81
8
A
LYS
65
-102.88
41.51
8
A
ASN
67
-51.04
86.68
9
A
TRP
11
-88.62
37.51
9
A
ASP
17
-103.74
75.35
9
A
GLU
21
34.11
41.73
9
A
GLN
26
-82.02
41.10
9
A
MET
36
33.99
37.06
9
A
SER
42
-160.49
112.53
9
A
THR
45
-84.22
40.83
9
A
GLU
53
-29.44
-49.77
9
A
ASN
55
-71.81
-74.57
9
A
LYS
65
33.16
47.61
10
A
ASP
17
-90.83
38.45
10
A
MET
36
39.02
42.56
10
A
SER
42
-115.89
-71.67
10
A
THR
45
-82.12
48.94
10
A
ASN
55
-90.80
-67.26
10
A
ASN
67
-86.29
40.59
10
A
SER
71
-44.96
165.30
11
A
SER
3
-174.18
147.74
11
A
GLU
21
-42.29
155.14
11
A
CYS
23
-45.93
166.91
11
A
TRP
27
34.23
42.95
11
A
LYS
28
-55.45
177.90
11
A
THR
45
34.58
42.04
11
A
LEU
48
-40.24
-70.38
11
A
PRO
70
-69.79
-176.74
12
A
SER
2
-101.95
42.56
12
A
LYS
12
-34.27
-35.63
12
A
ILE
24
-37.74
149.04
12
A
TRP
27
-37.93
128.82
12
A
ASN
44
-49.44
178.77
12
A
THR
45
-85.01
43.92
12
A
ASN
55
-98.41
-70.25
12
A
LYS
65
-67.08
97.82
13
A
SER
8
-54.89
108.38
13
A
ILE
24
-49.61
175.21
13
A
MET
36
39.26
50.63
13
A
ASN
44
-62.40
85.45
13
A
ASN
55
-80.91
-75.33
13
A
ASN
67
-59.83
87.85
13
A
SER
68
-166.72
107.73
13
A
PRO
70
-69.78
-174.75
14
A
SER
3
-42.13
151.59
14
A
SER
5
-124.54
-54.39
14
A
CYS
23
-52.46
-177.69
14
A
ILE
24
38.55
45.58
14
A
TRP
27
-40.93
150.77
14
A
LYS
28
-60.14
76.38
14
A
MET
36
34.07
44.90
14
A
THR
45
-86.71
41.67
14
A
ASN
67
-59.96
172.53
14
A
SER
68
-174.61
144.22
15
A
LYS
9
-82.57
38.50
15
A
TRP
11
-85.04
30.35
15
A
ILE
24
39.33
53.03
15
A
LEU
25
-45.58
155.73
15
A
ARG
33
-81.47
40.10
15
A
THR
45
-81.64
40.19
15
A
ASN
55
-102.08
-70.12
15
A
SER
71
-108.00
41.79
16
A
TRP
11
-93.67
33.58
16
A
TRP
27
-76.11
48.33
16
A
LYS
28
33.82
47.76
16
A
MET
36
34.49
45.59
16
A
SER
42
-122.75
-57.88
16
A
THR
45
36.21
44.14
16
A
GLU
53
-35.41
-37.25
16
A
ASN
55
-77.40
-74.10
16
A
PRO
70
-69.75
-176.84
17
A
TRP
11
-35.11
-38.06
17
A
TRP
27
-59.11
171.31
17
A
LYS
28
-64.29
85.63
17
A
THR
45
-86.07
48.87
17
A
SER
71
38.04
44.51
18
A
TRP
11
-89.28
31.39
18
A
CYS
23
-170.73
-176.74
18
A
ILE
24
-64.04
98.60
18
A
GLN
26
-82.45
38.55
18
A
TRP
27
33.72
46.39
18
A
LYS
28
-49.47
-179.44
18
A
MET
36
34.90
49.25
18
A
ASN
44
39.13
37.68
18
A
THR
45
34.36
40.40
18
A
GLU
58
-63.79
-71.21
18
A
GLU
59
-35.42
-34.31
18
A
ASN
67
-92.54
42.30
18
A
SER
71
34.66
42.27
19
A
LYS
9
-97.98
38.27
19
A
ASP
17
-106.42
48.06
19
A
LYS
28
-38.03
116.42
19
A
SER
42
-109.46
-68.44
19
A
ASN
44
-66.18
90.81
19
A
THR
45
38.92
45.19
19
A
LEU
48
-48.14
-73.74
19
A
GLU
53
-39.12
-29.71
19
A
ASN
55
-81.16
-76.25
19
A
PRO
70
-69.72
93.88
20
A
SER
3
-37.96
138.34
20
A
LYS
9
-79.88
45.72
20
A
ASN
19
-40.71
162.61
20
A
GLN
26
-49.48
176.03
20
A
TRP
27
-34.04
116.01
20
A
SER
42
-113.92
77.36
20
A
THR
45
-80.98
42.01
20
A
SER
66
-81.14
43.73
Solution Structure of the zinc finger BED domain of the zinc finger BED domain containing protein 1
1
N
N
2
N
N
A
VAL
10
A
VAL
10
HELX_P
A
LYS
12
A
LYS
12
5
1
3
A
SER
46
A
SER
46
HELX_P
A
LYS
54
A
LYS
54
1
2
9
A
PRO
57
A
PRO
57
HELX_P
A
PHE
63
A
PHE
63
1
3
7
metalc
2.331
A
CYS
32
A
SG
CYS
32
1_555
A
ZN
201
B
ZN
ZN
1_555
metalc
2.329
A
CYS
35
A
SG
CYS
35
1_555
A
ZN
201
B
ZN
ZN
1_555
metalc
2.345
A
HIS
51
A
NE2
HIS
51
1_555
A
ZN
201
B
ZN
ZN
1_555
metalc
2.328
A
HIS
56
A
NE2
HIS
56
1_555
A
ZN
201
B
ZN
ZN
1_555
TRANSCRIPTION
Zinc finger BED domain containing protein 1, dREF homolog, Putative c-like transposable element, structural genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, transcription
ZBED1_HUMAN
UNP
1
23
O96006
SKVWKYFGFDTNAEGCILQWKKIYCRICMAQIAYSGNTSNLSYHLEKNHPEEFCEFVKSN
23
82
2CT5
8
67
O96006
A
1
8
67
1
cloning artifact
GLY
1
2CT5
A
O96006
UNP
1
1
cloning artifact
SER
2
2CT5
A
O96006
UNP
2
1
cloning artifact
SER
3
2CT5
A
O96006
UNP
3
1
cloning artifact
GLY
4
2CT5
A
O96006
UNP
4
1
cloning artifact
SER
5
2CT5
A
O96006
UNP
5
1
cloning artifact
SER
6
2CT5
A
O96006
UNP
6
1
cloning artifact
GLY
7
2CT5
A
O96006
UNP
7
1
cloning artifact
SER
68
2CT5
A
O96006
UNP
68
1
cloning artifact
GLY
69
2CT5
A
O96006
UNP
69
1
cloning artifact
PRO
70
2CT5
A
O96006
UNP
70
1
cloning artifact
SER
71
2CT5
A
O96006
UNP
71
1
cloning artifact
SER
72
2CT5
A
O96006
UNP
72
1
cloning artifact
GLY
73
2CT5
A
O96006
UNP
73
3
anti-parallel
anti-parallel
A
PHE
14
A
PHE
14
A
GLY
15
A
GLY
15
A
ILE
30
A
ILE
30
A
CYS
32
A
CYS
32
A
ALA
37
A
ALA
37
A
ILE
39
A
ILE
39
BINDING SITE FOR RESIDUE ZN A 201
A
ZN
201
Software
4
A
CYS
32
A
CYS
32
4
1_555
A
CYS
35
A
CYS
35
4
1_555
A
HIS
51
A
HIS
51
4
1_555
A
HIS
56
A
HIS
56
4
1_555
1
P 1