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.
Kigawa, T.
Tomizawa, T.
Koshiba, S.
Inoue, 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
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
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 B-box domain of the human tripartite motif-containing 63 protein
10.2210/pdb2d8u/pdb
pdb_00002d8u
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
6784.683
Ubiquitin ligase TRIM63
6.3.2.-
zf-B box
1
man
polymer
65.409
ZINC ION
2
syn
non-polymer
Tripartite motif-containing 63, Muscle-specific RING finger protein 1, MuRF1, MURF-1, RING finger protein 28, Striated muscle RING zinc finger protein, Iris RING finger protein
no
no
GSSGSSGHPMCKEHEDEKINIYCLTCEVPTCSMCKVFGIHKACEVAPLQSVFQGQKTESGPSSG
GSSGSSGHPMCKEHEDEKINIYCLTCEVPTCSMCKVFGIHKACEVAPLQSVFQGQKTESGPSSG
A
hsi002010152.1
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
human
Homo
sample
Cell-free protein synthesis
TRIM63
9606
Homo sapiens
PLASMID
P050302-45
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
2006-06-08
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
_pdbx_nmr_spectrometer.model
_struct_conn.pdbx_dist_value
_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
2005-12-08
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
2.09mM zf-B_box U-13C, 15N; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.05mM ZNCl2; 1.0mM IDA; 90% H2O, 10% D2O
90% H2O/10% D2O
Bruker
collection
XwinNMR
3.5
Delaglio, F.
processing
NMRPipe
20031121
Johnson, B. A.
data analysis
NMRView
5.0.4
Kobayashi, N.
data analysis
KUJIRA
0.9321
Guntert, P.
structure solution
CYANA
2.0.17
Guntert, P.
refinement
CYANA
2.0.17
700
Bruker
AVANCE
ZN
201
2
ZN
ZN
201
A
ZN
401
2
ZN
ZN
401
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
HIS
8
n
8
HIS
8
A
PRO
9
n
9
PRO
9
A
MET
10
n
10
MET
10
A
CYS
11
n
11
CYS
11
A
LYS
12
n
12
LYS
12
A
GLU
13
n
13
GLU
13
A
HIS
14
n
14
HIS
14
A
GLU
15
n
15
GLU
15
A
ASP
16
n
16
ASP
16
A
GLU
17
n
17
GLU
17
A
LYS
18
n
18
LYS
18
A
ILE
19
n
19
ILE
19
A
ASN
20
n
20
ASN
20
A
ILE
21
n
21
ILE
21
A
TYR
22
n
22
TYR
22
A
CYS
23
n
23
CYS
23
A
LEU
24
n
24
LEU
24
A
THR
25
n
25
THR
25
A
CYS
26
n
26
CYS
26
A
GLU
27
n
27
GLU
27
A
VAL
28
n
28
VAL
28
A
PRO
29
n
29
PRO
29
A
THR
30
n
30
THR
30
A
CYS
31
n
31
CYS
31
A
SER
32
n
32
SER
32
A
MET
33
n
33
MET
33
A
CYS
34
n
34
CYS
34
A
LYS
35
n
35
LYS
35
A
VAL
36
n
36
VAL
36
A
PHE
37
n
37
PHE
37
A
GLY
38
n
38
GLY
38
A
ILE
39
n
39
ILE
39
A
HIS
40
n
40
HIS
40
A
LYS
41
n
41
LYS
41
A
ALA
42
n
42
ALA
42
A
CYS
43
n
43
CYS
43
A
GLU
44
n
44
GLU
44
A
VAL
45
n
45
VAL
45
A
ALA
46
n
46
ALA
46
A
PRO
47
n
47
PRO
47
A
LEU
48
n
48
LEU
48
A
GLN
49
n
49
GLN
49
A
SER
50
n
50
SER
50
A
VAL
51
n
51
VAL
51
A
PHE
52
n
52
PHE
52
A
GLN
53
n
53
GLN
53
A
GLY
54
n
54
GLY
54
A
GLN
55
n
55
GLN
55
A
LYS
56
n
56
LYS
56
A
THR
57
n
57
THR
57
A
GLU
58
n
58
GLU
58
A
SER
59
n
59
SER
59
A
GLY
60
n
60
GLY
60
A
PRO
61
n
61
PRO
61
A
SER
62
n
62
SER
62
A
SER
63
n
63
SER
63
A
GLY
64
n
64
GLY
64
A
author_defined_assembly
1
monomeric
A
CYS
11
A
SG
CYS
11
1_555
A
ZN
201
B
ZN
ZN
1_555
A
HIS
14
A
ND1
HIS
14
1_555
115.2
A
CYS
11
A
SG
CYS
11
1_555
A
ZN
201
B
ZN
ZN
1_555
A
CYS
31
A
SG
CYS
31
1_555
119.8
A
HIS
14
A
ND1
HIS
14
1_555
A
ZN
201
B
ZN
ZN
1_555
A
CYS
31
A
SG
CYS
31
1_555
109.4
A
CYS
11
A
SG
CYS
11
1_555
A
ZN
201
B
ZN
ZN
1_555
A
CYS
34
A
SG
CYS
34
1_555
107.4
A
HIS
14
A
ND1
HIS
14
1_555
A
ZN
201
B
ZN
ZN
1_555
A
CYS
34
A
SG
CYS
34
1_555
102.7
A
CYS
31
A
SG
CYS
31
1_555
A
ZN
201
B
ZN
ZN
1_555
A
CYS
34
A
SG
CYS
34
1_555
99.6
A
CYS
23
A
SG
CYS
23
1_555
A
ZN
401
C
ZN
ZN
1_555
A
CYS
26
A
SG
CYS
26
1_555
87.8
A
CYS
23
A
SG
CYS
23
1_555
A
ZN
401
C
ZN
ZN
1_555
A
HIS
40
A
ND1
HIS
40
1_555
119.7
A
CYS
26
A
SG
CYS
26
1_555
A
ZN
401
C
ZN
ZN
1_555
A
HIS
40
A
ND1
HIS
40
1_555
118.6
A
CYS
23
A
SG
CYS
23
1_555
A
ZN
401
C
ZN
ZN
1_555
A
CYS
43
A
SG
CYS
43
1_555
98.7
A
CYS
26
A
SG
CYS
26
1_555
A
ZN
401
C
ZN
ZN
1_555
A
CYS
43
A
SG
CYS
43
1_555
120.0
A
HIS
40
A
ND1
HIS
40
1_555
A
ZN
401
C
ZN
ZN
1_555
A
CYS
43
A
SG
CYS
43
1_555
109.2
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
TYR
22
A
N
TYR
22
A
O
ALA
46
A
O
ALA
46
1
A
SER
2
-131.05
-48.18
1
A
LEU
24
-108.26
-61.03
1
A
THR
25
-33.05
-70.02
1
A
GLU
27
70.77
53.48
1
A
PRO
29
-69.73
88.54
1
A
CYS
31
-68.62
-176.63
1
A
CYS
43
-65.59
-178.03
1
A
PRO
47
-69.76
89.78
1
A
LEU
48
-36.56
-32.95
1
A
GLN
53
-44.79
150.67
2
A
GLU
17
-60.00
92.21
2
A
LEU
24
-104.71
-61.43
2
A
PRO
29
-69.78
95.69
2
A
CYS
31
-57.04
171.42
2
A
ALA
42
-82.31
34.28
2
A
PRO
47
-69.74
85.24
2
A
PHE
52
-169.93
105.12
2
A
GLN
53
36.59
42.55
3
A
LEU
24
-104.05
-62.79
3
A
THR
25
-32.62
-73.86
3
A
HIS
40
-69.33
69.94
3
A
ALA
42
-82.91
34.20
3
A
GLN
49
-32.60
-72.91
3
A
VAL
51
33.02
53.28
3
A
GLN
55
35.50
45.39
3
A
GLU
58
-37.22
112.35
3
A
SER
59
-80.84
42.42
3
A
PRO
61
-69.78
86.90
4
A
LEU
24
-97.32
-64.17
4
A
THR
25
-29.90
-72.39
4
A
PRO
29
-69.74
91.74
4
A
HIS
40
-69.35
69.38
4
A
ALA
42
-83.17
32.00
4
A
PRO
47
-69.78
91.00
4
A
LEU
48
-39.33
-39.81
4
A
GLN
53
-39.06
126.80
4
A
GLN
55
-39.57
148.87
4
A
THR
57
-108.93
43.80
5
A
PRO
29
-69.76
83.89
5
A
CYS
31
-52.70
-174.88
5
A
PHE
37
-125.98
-58.61
5
A
HIS
40
-74.91
45.13
5
A
CYS
43
-65.04
-177.88
5
A
PRO
47
-69.76
95.06
5
A
LEU
48
-31.96
-36.73
5
A
GLN
49
-68.11
88.71
5
A
VAL
51
-57.90
98.89
5
A
GLN
55
36.62
41.35
5
A
LYS
56
-170.76
106.22
6
A
SER
2
-79.46
45.61
6
A
PRO
9
-69.75
-172.69
6
A
MET
10
-36.82
155.50
6
A
HIS
14
-57.87
-173.55
6
A
LYS
18
-32.84
115.32
6
A
ILE
19
-39.94
132.99
6
A
LEU
24
-109.87
-60.66
6
A
PRO
29
-69.70
88.18
6
A
CYS
31
-52.77
-174.08
6
A
ALA
42
-85.28
31.81
6
A
PRO
47
-69.78
89.78
6
A
SER
62
-69.46
96.33
7
A
PRO
29
-69.77
94.00
7
A
CYS
31
-53.38
-174.05
7
A
HIS
40
-82.11
36.67
7
A
CYS
43
-67.16
-175.48
7
A
PRO
47
-69.70
88.34
7
A
LEU
48
-32.92
-38.23
7
A
SER
50
70.12
54.14
7
A
VAL
51
-63.75
95.02
7
A
PHE
52
-134.93
-64.27
7
A
GLN
55
-34.53
136.58
7
A
SER
62
39.96
41.09
8
A
SER
3
-57.74
90.50
8
A
HIS
14
-58.39
-178.43
8
A
LYS
18
-33.89
131.70
8
A
LEU
24
-106.01
-60.34
8
A
THR
25
-33.88
-76.03
8
A
GLU
27
70.97
54.52
8
A
PRO
29
-69.78
86.45
8
A
CYS
31
-53.86
175.86
8
A
ALA
42
-81.64
34.03
8
A
SER
59
-66.17
97.54
8
A
SER
62
-94.71
41.57
9
A
SER
3
-163.66
115.28
9
A
SER
6
-79.53
45.69
9
A
CYS
11
-44.61
108.86
9
A
ASP
16
-86.47
-71.36
9
A
LEU
24
-103.28
-62.90
9
A
PRO
29
-69.74
89.41
9
A
CYS
31
-50.33
-176.27
9
A
CYS
34
-39.22
-25.01
9
A
ALA
42
-82.24
33.40
9
A
PRO
47
-69.77
89.70
9
A
LEU
48
-39.25
-36.38
9
A
GLN
49
-54.61
106.35
9
A
VAL
51
-38.58
98.45
9
A
GLN
53
-127.76
-52.19
9
A
SER
63
-104.65
44.22
10
A
LEU
24
-103.28
-61.33
10
A
THR
25
-33.34
-70.18
10
A
PRO
29
-69.74
85.97
10
A
CYS
31
-61.68
-176.95
10
A
ALA
42
-83.53
33.82
10
A
PRO
47
-69.77
87.42
10
A
GLN
49
-58.87
96.04
10
A
VAL
51
-53.25
95.81
10
A
PHE
52
-133.45
-64.23
10
A
PRO
61
-69.82
13.12
11
A
ASP
16
72.63
54.95
11
A
PRO
29
-69.79
99.50
11
A
CYS
31
-60.03
-174.36
11
A
ALA
42
-82.92
30.11
11
A
PRO
47
-69.73
82.38
11
A
GLN
49
-67.79
93.83
11
A
SER
50
74.47
53.48
11
A
VAL
51
-59.21
99.89
11
A
PHE
52
-127.96
-58.62
12
A
SER
3
39.98
42.49
12
A
GLU
17
-174.57
113.89
12
A
ILE
19
-34.19
113.44
12
A
THR
25
-36.59
-75.40
12
A
PRO
29
-69.72
99.27
12
A
MET
33
-37.98
-37.47
12
A
ALA
42
-83.50
33.37
12
A
THR
57
-36.17
143.43
13
A
HIS
14
-66.07
-173.88
13
A
LEU
24
-107.58
-60.96
13
A
PRO
29
-69.77
83.05
13
A
CYS
31
-53.83
-176.48
13
A
ALA
42
-82.38
33.98
13
A
LEU
48
-36.11
-31.64
13
A
SER
50
-124.49
-72.73
13
A
SER
63
-132.09
-62.25
14
A
LEU
24
-107.27
-62.29
14
A
PRO
29
-69.75
89.38
14
A
PRO
47
-69.73
92.56
14
A
GLN
49
-63.86
94.54
14
A
SER
50
73.21
47.18
14
A
GLU
58
-68.41
91.61
15
A
SER
5
-99.43
46.67
15
A
GLU
15
-106.20
-66.77
15
A
LYS
18
34.32
47.16
15
A
ILE
19
31.31
54.88
15
A
LEU
24
-100.29
-63.02
15
A
THR
25
-29.39
-76.20
15
A
HIS
40
-65.77
71.67
15
A
ALA
42
-87.93
33.39
15
A
LEU
48
-29.89
-50.72
15
A
GLN
53
-47.85
158.65
15
A
PRO
61
-69.77
90.06
16
A
PRO
29
-69.78
96.25
16
A
ALA
42
-81.98
34.24
16
A
LEU
48
-31.68
-36.82
16
A
VAL
51
-56.83
96.01
16
A
SER
59
-175.00
105.21
16
A
PRO
61
-69.77
0.83
17
A
SER
2
-162.04
118.59
17
A
PRO
9
-69.75
-173.93
17
A
CYS
11
-45.95
105.76
17
A
ILE
19
-33.60
110.74
17
A
LEU
24
-103.44
-61.82
17
A
THR
25
-29.67
-66.03
17
A
PRO
29
-69.79
97.24
17
A
CYS
31
-62.73
-177.44
17
A
HIS
40
-68.80
69.63
17
A
ALA
42
-82.83
33.89
17
A
LEU
48
-27.89
-44.32
17
A
PRO
61
-69.81
2.87
18
A
CYS
11
-46.81
156.32
18
A
LEU
24
-98.93
-61.02
18
A
THR
25
-32.56
-74.24
18
A
PRO
29
-69.81
92.34
18
A
CYS
31
-55.27
-174.44
18
A
HIS
40
-107.05
54.18
18
A
ALA
42
-83.14
32.59
18
A
PRO
47
-69.77
16.67
18
A
SER
50
31.38
47.61
18
A
PRO
61
-69.72
-173.82
19
A
SER
2
-59.59
104.84
19
A
GLU
13
-133.46
-36.05
19
A
LEU
24
-105.02
-61.39
19
A
THR
25
-33.62
-72.71
19
A
PRO
29
-69.78
81.87
19
A
ALA
42
-82.80
32.81
19
A
PRO
47
-69.76
91.83
19
A
LEU
48
-34.94
-36.70
19
A
GLN
49
-58.71
86.66
19
A
VAL
51
-38.54
102.09
19
A
PHE
52
-103.07
-63.59
19
A
GLN
53
-125.82
-61.02
19
A
SER
62
-81.33
44.34
20
A
HIS
8
-173.62
134.05
20
A
CYS
11
-51.63
98.42
20
A
LEU
24
-104.79
-61.51
20
A
HIS
40
-101.08
54.30
20
A
PRO
47
-69.75
87.61
Solution structure of the B-box domain of the human tripartite motif-containing 63 protein
1
N
N
2
N
N
2
N
N
A
SER
32
A
SER
32
HELX_P
A
PHE
37
A
PHE
37
1
1
6
metalc
2.315
A
CYS
11
A
SG
CYS
11
1_555
A
ZN
201
B
ZN
ZN
1_555
metalc
2.329
A
HIS
14
A
ND1
HIS
14
1_555
A
ZN
201
B
ZN
ZN
1_555
metalc
2.308
A
CYS
23
A
SG
CYS
23
1_555
A
ZN
401
C
ZN
ZN
1_555
metalc
2.272
A
CYS
26
A
SG
CYS
26
1_555
A
ZN
401
C
ZN
ZN
1_555
metalc
2.318
A
CYS
31
A
SG
CYS
31
1_555
A
ZN
201
B
ZN
ZN
1_555
metalc
2.320
A
CYS
34
A
SG
CYS
34
1_555
A
ZN
201
B
ZN
ZN
1_555
metalc
2.327
A
HIS
40
A
ND1
HIS
40
1_555
A
ZN
401
C
ZN
ZN
1_555
metalc
2.398
A
CYS
43
A
SG
CYS
43
1_555
A
ZN
401
C
ZN
ZN
1_555
LIGASE
tripartite motif-containing 63, TRIM63, Muscle-specific RING finger protein 1, MuRF1, RING finger protein 28, Striated muscle RING zinc finger protein, Iris ring finger protein, zf-B_box, structural genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Ligase
TRI63_HUMAN
UNP
1
119
Q969Q1
HPMCKEHEDEKINIYCLTCEVPTCSMCKVFGIHKACEVAPLQSVFQGQKTE
119
169
2D8U
8
58
Q969Q1
A
1
8
58
1
cloning artifact
GLY
1
2D8U
A
Q969Q1
UNP
1
1
cloning artifact
SER
2
2D8U
A
Q969Q1
UNP
2
1
cloning artifact
SER
3
2D8U
A
Q969Q1
UNP
3
1
cloning artifact
GLY
4
2D8U
A
Q969Q1
UNP
4
1
cloning artifact
SER
5
2D8U
A
Q969Q1
UNP
5
1
cloning artifact
SER
6
2D8U
A
Q969Q1
UNP
6
1
cloning artifact
GLY
7
2D8U
A
Q969Q1
UNP
7
1
cloning artifact
SER
59
2D8U
A
Q969Q1
UNP
59
1
cloning artifact
GLY
60
2D8U
A
Q969Q1
UNP
60
1
cloning artifact
PRO
61
2D8U
A
Q969Q1
UNP
61
1
cloning artifact
SER
62
2D8U
A
Q969Q1
UNP
62
1
cloning artifact
SER
63
2D8U
A
Q969Q1
UNP
63
1
cloning artifact
GLY
64
2D8U
A
Q969Q1
UNP
64
2
anti-parallel
A
TYR
22
A
TYR
22
A
CYS
23
A
CYS
23
A
VAL
45
A
VAL
45
A
ALA
46
A
ALA
46
BINDING SITE FOR RESIDUE ZN A 201
A
ZN
201
Software
5
BINDING SITE FOR RESIDUE ZN A 401
A
ZN
401
Software
4
A
CYS
11
A
CYS
11
5
1_555
A
HIS
14
A
HIS
14
5
1_555
A
GLU
17
A
GLU
17
5
1_555
A
CYS
31
A
CYS
31
5
1_555
A
CYS
34
A
CYS
34
5
1_555
A
CYS
23
A
CYS
23
4
1_555
A
CYS
26
A
CYS
26
4
1_555
A
HIS
40
A
HIS
40
4
1_555
A
CYS
43
A
CYS
43
4
1_555