1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Saito, K.
Koshiba, S.
Inoue, M.
Kigawa, T.
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 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 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
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 1st CAP-Gly domain in human cylindromatosis tumor suppressor CYLD
10.2210/pdb1whl/pdb
pdb_00001whl
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
10037.231
Cylindromatosis tumor suppressor CYLD
CAP-Gly domain
1
man
polymer
KIAA0849 protein
no
no
GSSGSSGIDVGCPVKVQLRSGEEKFPGVVRFRGPLLAERTVSGIFFGVELLEEGRGQGFTDGVYQGKQLFQCDEDCGVFV
ALDKLELIESGPSSG
GSSGSSGIDVGCPVKVQLRSGEEKFPGVVRFRGPLLAERTVSGIFFGVELLEEGRGQGFTDGVYQGKQLFQCDEDCGVFV
ALDKLELIESGPSSG
A
hsk001000012.1
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
human
Homo
sample
Cell-free Protein synthesis
Kazusa cDNA fh04363
9606
Homo sapiens
Plasmid
P031006-33
RIKEN Structural Genomics/Proteomics Initiative
RSGI
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
Version format compliance
Data collection
Database references
Derived calculations
1
0
2004-11-28
1
1
2008-04-30
1
2
2011-07-13
1
3
2022-03-02
_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
2004-05-28
REL
structures with the lowest energy
100
20
3D_13C-separated_NOESY
3D_15N-separated_NOESY
120mM
6.0
ambient
298
K
simulated annealing
1
lowest energy
1mM protein, 20mM sodium phosphate buffer, pH 6.0, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O
90% H2O/10% D2O
Bruker
collection
XwinNMR
2.6
Delaglio, F.
processing
NMRPipe
20020425
Johnson, B.A.
data analysis
NMRView
5
Brunger, A.T.
structure solution
CNS
1.1
Brunger, A.T.
refinement
CNS
1.1
800
Bruker
AVANCE
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
ILE
8
n
8
ILE
8
A
ASP
9
n
9
ASP
9
A
VAL
10
n
10
VAL
10
A
GLY
11
n
11
GLY
11
A
CYS
12
n
12
CYS
12
A
PRO
13
n
13
PRO
13
A
VAL
14
n
14
VAL
14
A
LYS
15
n
15
LYS
15
A
VAL
16
n
16
VAL
16
A
GLN
17
n
17
GLN
17
A
LEU
18
n
18
LEU
18
A
ARG
19
n
19
ARG
19
A
SER
20
n
20
SER
20
A
GLY
21
n
21
GLY
21
A
GLU
22
n
22
GLU
22
A
GLU
23
n
23
GLU
23
A
LYS
24
n
24
LYS
24
A
PHE
25
n
25
PHE
25
A
PRO
26
n
26
PRO
26
A
GLY
27
n
27
GLY
27
A
VAL
28
n
28
VAL
28
A
VAL
29
n
29
VAL
29
A
ARG
30
n
30
ARG
30
A
PHE
31
n
31
PHE
31
A
ARG
32
n
32
ARG
32
A
GLY
33
n
33
GLY
33
A
PRO
34
n
34
PRO
34
A
LEU
35
n
35
LEU
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
THR
40
n
40
THR
40
A
VAL
41
n
41
VAL
41
A
SER
42
n
42
SER
42
A
GLY
43
n
43
GLY
43
A
ILE
44
n
44
ILE
44
A
PHE
45
n
45
PHE
45
A
PHE
46
n
46
PHE
46
A
GLY
47
n
47
GLY
47
A
VAL
48
n
48
VAL
48
A
GLU
49
n
49
GLU
49
A
LEU
50
n
50
LEU
50
A
LEU
51
n
51
LEU
51
A
GLU
52
n
52
GLU
52
A
GLU
53
n
53
GLU
53
A
GLY
54
n
54
GLY
54
A
ARG
55
n
55
ARG
55
A
GLY
56
n
56
GLY
56
A
GLN
57
n
57
GLN
57
A
GLY
58
n
58
GLY
58
A
PHE
59
n
59
PHE
59
A
THR
60
n
60
THR
60
A
ASP
61
n
61
ASP
61
A
GLY
62
n
62
GLY
62
A
VAL
63
n
63
VAL
63
A
TYR
64
n
64
TYR
64
A
GLN
65
n
65
GLN
65
A
GLY
66
n
66
GLY
66
A
LYS
67
n
67
LYS
67
A
GLN
68
n
68
GLN
68
A
LEU
69
n
69
LEU
69
A
PHE
70
n
70
PHE
70
A
GLN
71
n
71
GLN
71
A
CYS
72
n
72
CYS
72
A
ASP
73
n
73
ASP
73
A
GLU
74
n
74
GLU
74
A
ASP
75
n
75
ASP
75
A
CYS
76
n
76
CYS
76
A
GLY
77
n
77
GLY
77
A
VAL
78
n
78
VAL
78
A
PHE
79
n
79
PHE
79
A
VAL
80
n
80
VAL
80
A
ALA
81
n
81
ALA
81
A
LEU
82
n
82
LEU
82
A
ASP
83
n
83
ASP
83
A
LYS
84
n
84
LYS
84
A
LEU
85
n
85
LEU
85
A
GLU
86
n
86
GLU
86
A
LEU
87
n
87
LEU
87
A
ILE
88
n
88
ILE
88
A
GLU
89
n
89
GLU
89
A
SER
90
n
90
SER
90
A
GLY
91
n
91
GLY
91
A
PRO
92
n
92
PRO
92
A
SER
93
n
93
SER
93
A
SER
94
n
94
SER
94
A
GLY
95
n
95
GLY
95
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
A
O
VAL
78
A
O
VAL
78
A
N
VAL
48
A
N
VAL
48
A
O
GLY
47
A
O
GLY
47
A
N
ARG
30
A
N
ARG
30
A
O
PHE
25
A
O
PHE
25
A
N
VAL
16
A
N
VAL
16
A
N
LYS
15
A
N
LYS
15
A
O
GLU
86
A
O
GLU
86
A
N
TYR
64
A
N
TYR
64
A
O
LYS
67
A
O
LYS
67
1
A
SER
5
-127.06
-67.06
1
A
SER
6
60.17
-172.89
1
A
GLU
23
-176.62
126.87
1
A
PRO
34
-56.67
-173.16
1
A
LEU
35
-148.57
-61.29
1
A
THR
40
-141.09
-61.49
1
A
GLN
57
-140.89
33.25
1
A
ASP
73
-68.78
-179.98
1
A
CYS
76
-130.10
-46.75
1
A
SER
90
-98.40
35.45
2
A
SER
6
-79.33
-77.62
2
A
PRO
34
-53.72
-176.98
2
A
LEU
35
-95.73
-63.58
2
A
SER
90
56.28
96.38
3
A
GLU
22
-120.45
-58.16
3
A
LEU
35
-124.10
-66.52
3
A
GLU
38
-137.03
-70.28
3
A
ARG
39
-145.45
-46.83
3
A
THR
40
-161.07
35.42
3
A
CYS
76
-129.93
-58.34
3
A
SER
93
59.61
172.63
4
A
SER
2
-170.36
126.94
4
A
SER
6
-155.27
-45.89
4
A
LEU
35
-121.02
-55.41
4
A
ALA
37
-143.62
33.03
4
A
SER
42
-146.25
-48.15
4
A
CYS
76
-130.06
-51.79
5
A
ALA
37
-146.26
48.02
5
A
GLU
38
-177.68
-40.59
5
A
THR
40
62.87
-78.95
5
A
SER
42
-168.73
109.75
6
A
PRO
34
-69.04
-177.95
6
A
ALA
37
60.66
79.01
6
A
GLN
57
-143.40
33.39
6
A
CYS
76
-130.07
-63.93
6
A
SER
90
-161.01
49.31
7
A
SER
5
-163.28
-45.61
7
A
THR
40
57.06
97.65
7
A
SER
42
-167.88
35.18
7
A
GLN
57
-141.47
31.36
8
A
SER
2
61.26
153.77
8
A
SER
3
58.18
179.60
8
A
ARG
19
-61.80
-174.78
8
A
SER
20
-93.00
48.37
8
A
GLU
22
-121.43
-51.93
8
A
CYS
76
-130.04
-49.28
9
A
SER
2
60.43
95.45
9
A
SER
5
-98.82
31.50
9
A
SER
20
-100.04
48.26
9
A
GLU
22
-128.95
-60.45
9
A
PRO
34
-54.96
-169.31
9
A
ALA
37
-168.70
77.42
9
A
SER
42
-107.07
-67.43
9
A
GLN
57
-140.90
43.84
9
A
SER
93
-161.06
-63.87
10
A
SER
5
-170.82
-51.02
10
A
SER
6
60.31
166.88
10
A
ARG
19
-69.42
-174.99
10
A
GLU
23
-176.66
131.56
10
A
LEU
36
59.92
176.96
10
A
ALA
37
-171.30
124.37
10
A
CYS
76
-125.18
-52.83
10
A
SER
90
-140.61
-68.52
10
A
SER
94
-161.98
89.42
11
A
SER
2
60.42
176.65
11
A
SER
3
-90.33
-65.85
11
A
SER
6
-92.01
-78.00
11
A
ARG
19
-68.98
-170.27
11
A
GLU
22
-101.62
-66.54
11
A
PRO
34
-54.74
-174.01
11
A
GLU
38
-67.15
-74.97
11
A
ARG
39
-131.14
-78.24
11
A
SER
42
-160.01
-60.64
11
A
SER
94
-149.01
-48.09
12
A
SER
6
59.84
-176.78
12
A
GLU
22
-133.38
-57.70
12
A
LEU
36
59.80
172.90
12
A
GLU
38
-91.59
-67.08
12
A
GLN
57
-145.40
35.19
12
A
SER
93
-66.51
99.52
12
A
SER
94
60.90
178.91
13
A
SER
3
-159.82
-45.33
13
A
SER
5
-150.26
-50.38
13
A
GLU
22
-101.94
-61.86
13
A
ARG
32
-160.85
119.39
13
A
ALA
37
-164.38
87.92
13
A
GLU
38
-115.43
-73.07
13
A
GLN
57
-141.69
37.63
13
A
CYS
76
-129.96
-51.65
13
A
SER
90
-92.89
-75.25
14
A
SER
2
-99.34
34.35
14
A
ARG
19
-68.45
-175.86
14
A
THR
40
-154.16
-47.81
14
A
CYS
76
-127.61
-55.84
15
A
GLU
22
-95.03
-61.97
15
A
ALA
37
-167.87
33.61
15
A
GLU
38
-170.33
-65.72
15
A
ARG
39
-176.13
-68.84
15
A
GLN
57
-140.97
33.38
15
A
GLN
68
-69.72
95.56
15
A
CYS
76
-129.57
-56.47
15
A
PRO
92
-54.15
-171.78
15
A
SER
94
-60.77
-73.11
16
A
SER
5
-96.34
-64.79
16
A
SER
6
-63.44
-172.21
16
A
GLU
22
-149.46
-58.46
16
A
LEU
36
60.62
-176.21
16
A
GLU
38
-97.29
-67.44
16
A
VAL
41
-97.64
33.78
16
A
GLN
57
-141.51
43.42
16
A
CYS
76
-129.87
-60.84
16
A
SER
94
-175.92
-43.61
17
A
ARG
19
-78.02
-169.84
17
A
GLU
22
-124.03
-52.86
17
A
GLU
23
-176.06
139.89
17
A
LEU
35
-120.08
-60.97
17
A
ALA
37
-162.25
111.69
17
A
GLU
38
-160.81
-58.71
17
A
GLN
57
-140.68
38.84
17
A
CYS
76
-121.46
-64.61
17
A
SER
94
-155.82
-54.87
18
A
SER
5
-159.09
31.95
18
A
GLU
22
-122.44
-65.09
18
A
GLU
38
-130.31
-68.43
18
A
GLN
57
-141.08
32.57
18
A
GLU
89
-121.36
-69.51
18
A
SER
90
-176.86
-40.17
19
A
SER
3
61.35
113.24
19
A
SER
20
-68.27
74.40
19
A
LEU
35
-153.01
-71.99
19
A
ARG
39
62.85
-79.61
19
A
SER
42
60.21
100.73
19
A
GLN
57
-140.25
34.54
19
A
GLN
68
-68.08
89.99
19
A
CYS
76
-130.03
-58.80
19
A
SER
90
59.78
110.60
20
A
SER
5
-168.73
-69.88
20
A
SER
6
-60.41
-173.30
20
A
ILE
8
-68.39
94.95
20
A
GLU
22
-130.00
-66.40
20
A
PRO
34
-54.76
-170.26
20
A
LEU
35
-115.94
-71.67
20
A
SER
42
-176.39
68.63
Solution structure of the 1st CAP-Gly domain in human cylindromatosis tumor suppressor CYLD
1
N
N
A
ALA
81
A
ALA
81
HELX_P
A
ASP
83
A
ASP
83
5
1
3
ANTITUMOR PROTEIN
Tumor suppressor, deubiquitinating enzyme, structural genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, ANTITUMOR PROTEIN
CYLD_HUMAN
UNP
1
132
Q9NQC7
IDVGCPVKVQLRSGEEKFPGVVRFRGPLLAERTVSGIFFGVELLEEGRGQGFTDGVYQGKQLFQCDEDCGVFVALDKLEL
IE
132
213
1WHL
8
89
Q9NQC7
A
1
8
89
1
cloning artifact
GLY
1
1WHL
A
Q9NQC7
UNP
1
1
cloning artifact
SER
2
1WHL
A
Q9NQC7
UNP
2
1
cloning artifact
SER
3
1WHL
A
Q9NQC7
UNP
3
1
cloning artifact
GLY
4
1WHL
A
Q9NQC7
UNP
4
1
cloning artifact
SER
5
1WHL
A
Q9NQC7
UNP
5
1
cloning artifact
SER
6
1WHL
A
Q9NQC7
UNP
6
1
cloning artifact
GLY
7
1WHL
A
Q9NQC7
UNP
7
1
cloning artifact
SER
90
1WHL
A
Q9NQC7
UNP
90
1
cloning artifact
GLY
91
1WHL
A
Q9NQC7
UNP
91
1
cloning artifact
PRO
92
1WHL
A
Q9NQC7
UNP
92
1
cloning artifact
SER
93
1WHL
A
Q9NQC7
UNP
93
1
cloning artifact
SER
94
1WHL
A
Q9NQC7
UNP
94
1
cloning artifact
GLY
95
1WHL
A
Q9NQC7
UNP
95
5
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
GLY
77
A
GLY
77
A
VAL
80
A
VAL
80
A
PHE
46
A
PHE
46
A
LEU
50
A
LEU
50
A
LYS
24
A
LYS
24
A
ARG
32
A
ARG
32
A
PRO
13
A
PRO
13
A
GLN
17
A
GLN
17
A
LEU
85
A
LEU
85
A
LEU
87
A
LEU
87
A
VAL
63
A
VAL
63
A
TYR
64
A
TYR
64
A
LYS
67
A
LYS
67
A
GLN
68
A
GLN
68