1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Tashiro, M.
Okubo, S.
Shimotakahara, S.
Hatanaka, H.
Yasuda, H.
Kainosho, M.
Yokoyama, S.
Shindo, H.
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
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
NE
J.Biomol.NMR
JBNME9
0800
0925-2738
25
153
156
10.1023/A:1022254432039
12652124
NMR structure of ubiquitin-like domain in PARKIN: Gene product of familial Parkinson's disease.
2003
UK
Nature
NATUAS
0006
0028-0836
392
605
608
10.1038/33416
Mutations in the parkin gene causes autosomal recessive
juvenile parkinsonism
1998
10.2210/pdb1mg8/pdb
pdb_00001mg8
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
8918.294
Parkin
ubiquitin-like domain
1
nat
polymer
no
no
MGMIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRRR
MGMIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRRR
A
trt001000160.1
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
house mouse
Mus
sample
10090
Mus musculus
pET28b
BL21 (DE3)
RIKEN Structural Genomics/Proteomics Initiative
RSGI
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Database references
1
0
2003-04-08
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
1
4
2022-12-21
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_ref_seq_dif.details
Y
RCSB
Y
PDBJ
2002-08-15
REL
REL
The structure was determined using triple-resonance NMR spectroscopy.
structures with the lowest energy
50
10
3D_13C-separated_NOESY
3D_15N-separated_NOESY
5.0
ambient
298
K
simulated annealing
1mM ubiquitin-like domain U-15N,13C; 25mM acetate buffer NA, 2mM dithiothreitol-d10
90% H2O/10% D2O
refinement
X-PLOR
processing
NMRPipe
500
Bruker
DMX
600
Bruker
DRX
600
Varian
INOVA
MET
1
n
1
MET
1
A
GLY
2
n
2
GLY
2
A
MET
3
n
3
MET
3
A
ILE
4
n
4
ILE
4
A
VAL
5
n
5
VAL
5
A
PHE
6
n
6
PHE
6
A
VAL
7
n
7
VAL
7
A
ARG
8
n
8
ARG
8
A
PHE
9
n
9
PHE
9
A
ASN
10
n
10
ASN
10
A
SER
11
n
11
SER
11
A
SER
12
n
12
SER
12
A
TYR
13
n
13
TYR
13
A
GLY
14
n
14
GLY
14
A
PHE
15
n
15
PHE
15
A
PRO
16
n
16
PRO
16
A
VAL
17
n
17
VAL
17
A
GLU
18
n
18
GLU
18
A
VAL
19
n
19
VAL
19
A
ASP
20
n
20
ASP
20
A
SER
21
n
21
SER
21
A
ASP
22
n
22
ASP
22
A
THR
23
n
23
THR
23
A
SER
24
n
24
SER
24
A
ILE
25
n
25
ILE
25
A
LEU
26
n
26
LEU
26
A
GLN
27
n
27
GLN
27
A
LEU
28
n
28
LEU
28
A
LYS
29
n
29
LYS
29
A
GLU
30
n
30
GLU
30
A
VAL
31
n
31
VAL
31
A
VAL
32
n
32
VAL
32
A
ALA
33
n
33
ALA
33
A
LYS
34
n
34
LYS
34
A
ARG
35
n
35
ARG
35
A
GLN
36
n
36
GLN
36
A
GLY
37
n
37
GLY
37
A
VAL
38
n
38
VAL
38
A
PRO
39
n
39
PRO
39
A
ALA
40
n
40
ALA
40
A
ASP
41
n
41
ASP
41
A
GLN
42
n
42
GLN
42
A
LEU
43
n
43
LEU
43
A
ARG
44
n
44
ARG
44
A
VAL
45
n
45
VAL
45
A
ILE
46
n
46
ILE
46
A
PHE
47
n
47
PHE
47
A
ALA
48
n
48
ALA
48
A
GLY
49
n
49
GLY
49
A
LYS
50
n
50
LYS
50
A
GLU
51
n
51
GLU
51
A
LEU
52
n
52
LEU
52
A
PRO
53
n
53
PRO
53
A
ASN
54
n
54
ASN
54
A
HIS
55
n
55
HIS
55
A
LEU
56
n
56
LEU
56
A
THR
57
n
57
THR
57
A
VAL
58
n
58
VAL
58
A
GLN
59
n
59
GLN
59
A
ASN
60
n
60
ASN
60
A
CYS
61
n
61
CYS
61
A
ASP
62
n
62
ASP
62
A
LEU
63
n
63
LEU
63
A
GLU
64
n
64
GLU
64
A
GLN
65
n
65
GLN
65
A
GLN
66
n
66
GLN
66
A
SER
67
n
67
SER
67
A
ILE
68
n
68
ILE
68
A
VAL
69
n
69
VAL
69
A
HIS
70
n
70
HIS
70
A
ILE
71
n
71
ILE
71
A
VAL
72
n
72
VAL
72
A
GLN
73
n
73
GLN
73
A
ARG
74
n
74
ARG
74
A
PRO
75
n
75
PRO
75
A
ARG
76
n
76
ARG
76
A
ARG
77
n
77
ARG
77
A
ARG
78
n
78
ARG
78
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
17
A
O
VAL
17
A
N
VAL
5
A
N
VAL
5
A
N
PHE
6
A
N
PHE
6
A
O
VAL
69
A
O
VAL
69
A
O
HIS
70
A
O
HIS
70
A
N
ILE
46
A
N
ILE
46
1
A
ARG
8
0.311
SIDE CHAIN
1
A
ARG
74
0.224
SIDE CHAIN
1
A
ARG
76
0.280
SIDE CHAIN
1
A
ARG
77
0.265
SIDE CHAIN
1
A
ARG
78
0.244
SIDE CHAIN
2
A
ARG
8
0.167
SIDE CHAIN
2
A
ARG
35
0.301
SIDE CHAIN
2
A
ARG
44
0.133
SIDE CHAIN
2
A
ARG
74
0.275
SIDE CHAIN
2
A
ARG
76
0.138
SIDE CHAIN
2
A
ARG
77
0.292
SIDE CHAIN
2
A
ARG
78
0.230
SIDE CHAIN
3
A
ARG
8
0.295
SIDE CHAIN
3
A
ARG
35
0.305
SIDE CHAIN
3
A
ARG
44
0.299
SIDE CHAIN
3
A
ARG
74
0.163
SIDE CHAIN
3
A
ARG
76
0.140
SIDE CHAIN
3
A
ARG
77
0.220
SIDE CHAIN
3
A
ARG
78
0.310
SIDE CHAIN
4
A
ARG
8
0.308
SIDE CHAIN
4
A
ARG
35
0.309
SIDE CHAIN
4
A
ARG
44
0.318
SIDE CHAIN
4
A
ARG
74
0.304
SIDE CHAIN
4
A
ARG
76
0.245
SIDE CHAIN
4
A
ARG
77
0.318
SIDE CHAIN
4
A
ARG
78
0.314
SIDE CHAIN
5
A
ARG
8
0.318
SIDE CHAIN
5
A
ARG
35
0.168
SIDE CHAIN
5
A
ARG
44
0.299
SIDE CHAIN
5
A
ARG
74
0.275
SIDE CHAIN
5
A
ARG
76
0.301
SIDE CHAIN
5
A
ARG
77
0.317
SIDE CHAIN
5
A
ARG
78
0.276
SIDE CHAIN
6
A
ARG
8
0.281
SIDE CHAIN
6
A
ARG
35
0.297
SIDE CHAIN
6
A
ARG
44
0.232
SIDE CHAIN
6
A
ARG
74
0.310
SIDE CHAIN
6
A
ARG
76
0.313
SIDE CHAIN
6
A
ARG
77
0.210
SIDE CHAIN
6
A
ARG
78
0.287
SIDE CHAIN
7
A
ARG
8
0.289
SIDE CHAIN
7
A
ARG
35
0.299
SIDE CHAIN
7
A
ARG
44
0.310
SIDE CHAIN
7
A
ARG
74
0.302
SIDE CHAIN
7
A
ARG
76
0.140
SIDE CHAIN
7
A
ARG
77
0.317
SIDE CHAIN
8
A
ARG
8
0.271
SIDE CHAIN
8
A
ARG
35
0.304
SIDE CHAIN
8
A
ARG
44
0.228
SIDE CHAIN
8
A
ARG
74
0.255
SIDE CHAIN
8
A
ARG
76
0.298
SIDE CHAIN
8
A
ARG
77
0.261
SIDE CHAIN
8
A
ARG
78
0.316
SIDE CHAIN
9
A
ARG
8
0.262
SIDE CHAIN
9
A
ARG
35
0.278
SIDE CHAIN
9
A
ARG
44
0.315
SIDE CHAIN
9
A
ARG
74
0.282
SIDE CHAIN
9
A
ARG
76
0.308
SIDE CHAIN
9
A
ARG
77
0.254
SIDE CHAIN
9
A
ARG
78
0.203
SIDE CHAIN
10
A
ARG
8
0.292
SIDE CHAIN
10
A
ARG
35
0.264
SIDE CHAIN
10
A
ARG
44
0.091
SIDE CHAIN
10
A
ARG
74
0.084
SIDE CHAIN
10
A
ARG
76
0.219
SIDE CHAIN
10
A
ARG
77
0.294
SIDE CHAIN
10
A
ARG
78
0.202
SIDE CHAIN
9
-5.05
0.70
120.80
115.75
A
A
A
CB
CG
CD2
PHE
PHE
PHE
9
9
9
N
1
A
PHE
9
-68.89
96.64
1
A
ASN
10
61.61
-131.31
1
A
SER
12
77.60
-1.43
1
A
SER
24
-60.84
-142.40
1
A
ILE
25
-130.17
-31.11
1
A
ALA
48
59.61
7.76
1
A
ASP
62
103.78
30.63
1
A
GLU
64
59.96
152.41
1
A
GLN
66
74.60
106.40
1
A
SER
67
-171.81
130.38
1
A
ARG
74
-39.57
96.95
1
A
ARG
77
-54.12
92.98
2
A
ASN
10
62.12
-90.78
2
A
SER
11
-128.35
-71.12
2
A
SER
24
-61.24
-142.61
2
A
ASP
62
155.02
36.61
2
A
GLU
64
46.99
-154.34
2
A
GLN
66
74.39
109.35
2
A
SER
67
-175.87
129.84
2
A
ARG
74
-53.64
108.35
2
A
ARG
77
-53.70
92.28
3
A
ASN
10
54.46
162.99
3
A
SER
11
34.89
-109.21
3
A
TYR
13
-48.12
153.74
3
A
SER
24
69.31
-142.81
3
A
ILE
25
-144.15
-25.50
3
A
ASP
62
109.13
32.77
3
A
GLU
64
51.60
-157.51
3
A
GLN
66
80.23
111.54
3
A
SER
67
-173.34
129.72
3
A
ARG
77
-55.90
90.79
4
A
ASN
10
61.62
-91.04
4
A
SER
11
-165.30
-63.76
4
A
TYR
13
-105.30
-160.92
4
A
ILE
25
72.35
-30.57
4
A
ALA
48
55.66
7.74
4
A
ASP
62
103.26
37.45
4
A
LEU
63
-66.60
-83.23
4
A
GLU
64
76.45
162.26
4
A
GLN
66
76.00
112.30
4
A
SER
67
-163.18
118.58
4
A
ARG
74
-48.24
105.02
4
A
ARG
77
-56.42
92.33
5
A
ASN
10
68.18
-84.62
5
A
SER
11
-177.20
-32.09
5
A
SER
24
65.78
-144.53
5
A
ILE
25
-144.94
-28.26
5
A
GLU
51
-48.36
88.75
5
A
LEU
56
-42.47
162.74
5
A
ASP
62
105.56
36.07
5
A
GLU
64
62.94
144.33
5
A
GLN
65
-37.14
135.83
5
A
GLN
66
73.59
105.55
5
A
ARG
74
-56.09
109.12
5
A
ARG
77
-55.88
92.06
6
A
ASN
10
66.77
-82.91
6
A
SER
11
179.30
-31.54
6
A
SER
24
-60.61
-135.98
6
A
ILE
25
-135.81
-33.38
6
A
ASP
62
106.56
31.16
6
A
GLU
64
61.96
165.26
6
A
GLN
66
75.27
108.23
6
A
ARG
77
-55.94
91.83
7
A
ASN
10
58.27
-92.39
7
A
SER
11
-145.95
-83.34
7
A
ILE
25
72.04
-35.07
7
A
GLU
51
-48.48
96.88
7
A
PRO
53
-72.81
-160.49
7
A
ASP
62
90.49
33.72
7
A
GLU
64
51.86
-154.61
7
A
GLN
66
72.90
106.25
7
A
SER
67
-175.41
131.93
7
A
ARG
77
-56.47
91.66
8
A
ASN
10
-32.86
150.57
8
A
SER
11
79.47
-141.28
8
A
ILE
25
72.16
-32.66
8
A
ALA
48
59.41
9.61
8
A
ASP
62
100.47
34.07
8
A
GLU
64
60.31
151.28
8
A
GLN
65
-33.89
127.51
8
A
GLN
66
74.58
110.18
8
A
ARG
77
-55.95
92.14
9
A
ASN
10
-36.69
147.98
9
A
SER
11
78.08
-145.06
9
A
SER
24
-60.01
-131.56
9
A
ILE
25
-139.69
-32.87
9
A
ALA
48
59.35
7.33
9
A
ASP
62
105.43
30.88
9
A
GLU
64
56.87
163.59
9
A
GLN
65
-37.85
122.84
9
A
GLN
66
73.97
107.89
9
A
ARG
74
-37.65
98.01
9
A
ARG
77
-54.17
91.67
10
A
ASN
10
-39.99
153.46
10
A
SER
11
72.96
-151.06
10
A
SER
24
-56.78
-149.02
10
A
PRO
53
-77.75
-164.29
10
A
ASP
62
107.12
31.88
10
A
LEU
63
-72.90
-77.84
10
A
GLU
64
71.24
159.47
10
A
GLN
65
-37.99
122.62
10
A
GLN
66
75.82
108.95
10
A
ARG
74
-51.20
107.15
10
A
ARG
77
-55.37
92.32
NMR structure of ubiquitin-like domain in murine Parkin
1
N
N
A
ILE
25
A
ILE
25
HELX_P
A
GLY
37
A
GLY
37
1
1
13
APOPTOSIS
parkinson disease, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, APOPTOSIS
PRKN2_MOUSE
UNP
1
1
Q9WVS6
MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRRR
1
76
1MG8
3
78
Q9WVS6
A
1
3
78
1
initiating methionine
MET
1
1MG8
A
Q9WVS6
UNP
1
1
cloning artifact
GLY
2
1MG8
A
Q9WVS6
UNP
2
4
anti-parallel
parallel
anti-parallel
A
GLY
14
A
GLY
14
A
GLU
18
A
GLU
18
A
ILE
4
A
ILE
4
A
ARG
8
A
ARG
8
A
ILE
68
A
ILE
68
A
ILE
71
A
ILE
71
A
VAL
45
A
VAL
45
A
PHE
47
A
PHE
47