1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Zhao, C.
Kigawa, T.
Sato, M.
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
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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
To be Published
0353
Solution Structure of the Second UBA Domain in the Human Ubiquitin Specific Protease 5 (Isopeptidase 5)
10.2210/pdb2dak/pdb
pdb_00002dak
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
6519.079
Ubiquitin carboxyl-terminal hydrolase 5
3.1.2.15
UBA domain
1
man
polymer
Ubiquitin thiolesterase 5, Ubiquitin-specific processing protease 5, Deubiquitinating enzyme 5, Isopeptidase T
no
no
GSSGSSGPPEDCVTTIVSMGFSRDQALKALRATNNSLERAVDWIFSHIDDLDAEAAMSGPSSG
GSSGSSGPPEDCVTTIVSMGFSRDQALKALRATNNSLERAVDWIFSHIDDLDAEAAMSGPSSG
A
hsi002005673.2
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
human
Homo
sample
Cell-free protein synthesis
USP5
9606
Homo sapiens
Cell free synthesis
PLASMID
P050704-16
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_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2006-06-14
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_ref_seq_dif.details
Y
PDBJ
Y
PDBJ
2005-12-14
REL
target function, structures with the least restraint violations
100
20
3D_15N-separated_NOESY
3D_13C-separated_NOESY
120mM
7.0
ambient
296.0
K
torsion angle dynamics, restrainted molecular dynamics
1
lowest energy
0.84mM UBA domain U-15N, 13C; 20mM d-Tris-HCl (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
90% H2O/10% D2O
Bruker Bruker
collection
XwinNMR
2.6
Delaglio, F.
processing
NMRPipe
20030801
Johnson, B. A.
data analysis
NMRView
5.0.4
Kobayashi, N.
data analysis
KUJIRA
0.9321
Guntert, P.
structure solution
CYANA
1.0.8
Guntert, P.
refinement
CYANA
1.0.8
700
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
PRO
8
n
8
PRO
8
A
PRO
9
n
9
PRO
9
A
GLU
10
n
10
GLU
10
A
ASP
11
n
11
ASP
11
A
CYS
12
n
12
CYS
12
A
VAL
13
n
13
VAL
13
A
THR
14
n
14
THR
14
A
THR
15
n
15
THR
15
A
ILE
16
n
16
ILE
16
A
VAL
17
n
17
VAL
17
A
SER
18
n
18
SER
18
A
MET
19
n
19
MET
19
A
GLY
20
n
20
GLY
20
A
PHE
21
n
21
PHE
21
A
SER
22
n
22
SER
22
A
ARG
23
n
23
ARG
23
A
ASP
24
n
24
ASP
24
A
GLN
25
n
25
GLN
25
A
ALA
26
n
26
ALA
26
A
LEU
27
n
27
LEU
27
A
LYS
28
n
28
LYS
28
A
ALA
29
n
29
ALA
29
A
LEU
30
n
30
LEU
30
A
ARG
31
n
31
ARG
31
A
ALA
32
n
32
ALA
32
A
THR
33
n
33
THR
33
A
ASN
34
n
34
ASN
34
A
ASN
35
n
35
ASN
35
A
SER
36
n
36
SER
36
A
LEU
37
n
37
LEU
37
A
GLU
38
n
38
GLU
38
A
ARG
39
n
39
ARG
39
A
ALA
40
n
40
ALA
40
A
VAL
41
n
41
VAL
41
A
ASP
42
n
42
ASP
42
A
TRP
43
n
43
TRP
43
A
ILE
44
n
44
ILE
44
A
PHE
45
n
45
PHE
45
A
SER
46
n
46
SER
46
A
HIS
47
n
47
HIS
47
A
ILE
48
n
48
ILE
48
A
ASP
49
n
49
ASP
49
A
ASP
50
n
50
ASP
50
A
LEU
51
n
51
LEU
51
A
ASP
52
n
52
ASP
52
A
ALA
53
n
53
ALA
53
A
GLU
54
n
54
GLU
54
A
ALA
55
n
55
ALA
55
A
ALA
56
n
56
ALA
56
A
MET
57
n
57
MET
57
A
SER
58
n
58
SER
58
A
GLY
59
n
59
GLY
59
A
PRO
60
n
60
PRO
60
A
SER
61
n
61
SER
61
A
SER
62
n
62
SER
62
A
GLY
63
n
63
GLY
63
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
A
O
H
THR
SER
14
18
1.54
1
A
A
O
H
GLN
ALA
25
29
1.54
1
A
A
O
H
ARG
TRP
39
43
1.56
2
A
A
O
H
THR
SER
14
18
1.52
3
A
A
O
H
THR
SER
14
18
1.51
3
A
A
O
H
GLN
ALA
25
29
1.55
3
A
A
O
H
LEU
ASN
30
35
1.58
4
A
A
O
H
THR
SER
14
18
1.50
4
A
A
O
H
GLU
THR
10
14
1.52
4
A
A
O
H
GLN
ALA
25
29
1.55
4
A
A
O
H
LEU
ASN
30
35
1.56
4
A
A
O
H
ARG
TRP
39
43
1.57
4
A
A
O
H
LYS
ALA
28
32
1.58
5
A
A
O
H
THR
SER
14
18
1.51
5
A
A
O
H
GLN
ALA
25
29
1.55
5
A
A
O
H
ARG
TRP
39
43
1.56
6
A
A
O
H
THR
SER
14
18
1.51
6
A
A
O
H
GLN
ALA
25
29
1.56
6
A
A
O
H
ARG
TRP
39
43
1.57
6
A
A
O
H
LYS
ALA
28
32
1.58
7
A
A
O
H
THR
SER
14
18
1.50
7
A
A
O
H
ASP
LYS
24
28
1.52
7
A
A
O
H
ARG
TRP
39
43
1.54
7
A
A
O
H
GLU
THR
10
14
1.54
7
A
A
O
H
GLN
ALA
25
29
1.58
7
A
A
O
H
LEU
ASN
30
35
1.58
7
A
A
O
H
SER
ALA
36
40
1.59
8
A
A
O
H
GLN
ALA
25
29
1.54
8
A
A
O
H
ALA
THR
29
33
1.58
9
A
A
O
H
THR
SER
14
18
1.50
9
A
A
O
H
ALA
THR
29
33
1.56
9
A
A
O
H
LYS
ALA
28
32
1.57
9
A
A
O
H
ALA
ILE
40
44
1.58
9
A
A
O
H
GLN
ALA
25
29
1.59
10
A
A
O
H
GLN
ALA
25
29
1.53
10
A
A
O
H
THR
SER
14
18
1.57
10
A
A
O
H
ALA
THR
29
33
1.57
11
A
A
O
H
THR
SER
14
18
1.50
11
A
A
O
H
GLN
ALA
25
29
1.51
11
A
A
O
H
ALA
THR
29
33
1.57
12
A
A
O
H
THR
SER
14
18
1.51
12
A
A
O
H
ARG
TRP
39
43
1.53
12
A
A
O
H
LEU
THR
30
33
1.56
12
A
A
O
H
ASP
LYS
24
28
1.57
12
A
A
O
H
LEU
ASN
30
35
1.58
12
A
A
O
H
GLN
ALA
25
29
1.60
13
A
A
O
H
THR
SER
14
18
1.54
13
A
A
O
H
GLU
THR
10
14
1.55
13
A
A
O
H
ALA
ILE
40
44
1.55
13
A
A
O
H
ALA
THR
29
33
1.56
13
A
A
O
H
GLN
ALA
25
29
1.58
14
A
A
O
H
THR
SER
14
18
1.50
14
A
A
O
H
GLN
ALA
25
29
1.55
14
A
A
O
H
ALA
THR
29
33
1.57
15
A
A
O
H
GLU
THR
10
14
1.51
15
A
A
O
H
GLN
ALA
25
29
1.53
15
A
A
O
H
THR
SER
14
18
1.53
15
A
A
O
H
ALA
THR
29
33
1.56
15
A
A
O
H
SER
ALA
36
40
1.59
15
A
A
O
H
LYS
ALA
28
32
1.59
16
A
A
O
H
THR
SER
14
18
1.50
16
A
A
O
H
GLN
ALA
25
29
1.55
16
A
A
O
H
ALA
THR
29
33
1.60
17
A
A
O
H
ASP
LYS
24
28
1.50
17
A
A
O
H
THR
SER
14
18
1.54
17
A
A
O
H
ARG
TRP
39
43
1.55
17
A
A
O
H
LEU
ASN
30
35
1.57
17
A
A
O
H
GLN
ALA
25
29
1.58
18
A
A
O
H
THR
SER
14
18
1.50
18
A
A
O
H
GLN
ALA
25
29
1.54
18
A
A
O
H
LEU
ASN
30
35
1.56
18
A
A
O
H
SER
ALA
36
40
1.56
19
A
A
O
H
THR
SER
14
18
1.50
19
A
A
O
H
LEU
ASN
30
35
1.54
19
A
A
O
H
ARG
TRP
39
43
1.55
19
A
A
O
H
GLN
ALA
25
29
1.55
19
A
A
O
H
SER
ALA
36
40
1.55
20
A
A
O
H
GLN
ALA
25
29
1.53
20
A
A
O
H
THR
SER
14
18
1.54
20
A
A
O
H
ASP
LYS
24
28
1.57
20
A
A
O
H
ALA
THR
29
33
1.58
20
A
A
O
H
ASP
THR
11
15
1.59
1
A
SER
3
-178.16
88.46
1
A
SER
6
-47.79
160.22
1
A
ASP
50
168.44
-38.01
1
A
LEU
51
-67.73
78.76
1
A
GLU
54
-41.63
157.48
1
A
SER
61
-178.93
123.71
2
A
SER
5
-179.94
-59.31
2
A
SER
6
-152.00
83.02
2
A
ASN
35
48.97
70.56
2
A
ASP
52
-140.11
-55.52
2
A
ALA
53
51.17
73.22
2
A
ALA
56
-164.15
88.10
3
A
SER
3
62.97
111.90
3
A
SER
6
58.31
102.22
3
A
THR
33
-102.30
45.35
3
A
ASN
35
65.17
69.87
3
A
ASP
50
-116.44
77.18
3
A
ALA
53
-177.63
80.38
3
A
GLU
54
73.64
-58.61
3
A
ALA
55
51.31
97.71
3
A
ALA
56
-161.56
112.50
3
A
MET
57
58.44
87.30
4
A
SER
5
-67.02
79.46
4
A
THR
33
-88.99
40.16
4
A
ASN
35
65.61
82.63
4
A
ASP
50
179.89
106.96
4
A
GLU
54
-165.18
113.45
4
A
SER
61
-42.83
163.39
4
A
SER
62
48.03
92.12
5
A
ASN
35
61.49
66.66
5
A
ASP
50
60.40
103.33
5
A
ALA
55
51.25
97.37
5
A
ALA
56
-64.91
91.86
5
A
SER
61
56.48
108.00
5
A
SER
62
178.36
147.67
6
A
SER
5
-123.10
-58.51
6
A
THR
33
-97.43
43.02
6
A
ILE
44
-72.47
-70.98
6
A
ASP
50
65.63
107.28
6
A
ASP
52
49.45
94.00
6
A
ALA
53
-161.77
63.26
6
A
GLU
54
58.07
80.13
6
A
SER
58
70.07
-62.80
6
A
SER
62
59.74
152.41
7
A
SER
3
-148.01
-59.45
7
A
SER
6
59.73
152.56
7
A
ASN
35
61.69
79.92
7
A
ASP
49
-169.89
96.86
7
A
ASP
52
60.18
109.00
7
A
SER
61
-171.04
117.46
8
A
SER
3
-160.41
-58.59
8
A
SER
5
-122.68
-57.90
8
A
THR
33
-89.03
40.19
8
A
ASN
35
58.38
71.51
8
A
ALA
53
-131.98
-46.28
8
A
GLU
54
-173.06
81.84
8
A
ALA
55
-166.50
-59.19
9
A
SER
3
-162.16
99.94
9
A
SER
5
-156.76
76.88
9
A
SER
6
-143.05
-60.96
9
A
ILE
16
-54.31
-71.71
9
A
THR
33
-89.02
40.16
9
A
ASN
35
40.46
80.02
9
A
ILE
44
-54.46
-71.81
9
A
LEU
51
-67.32
75.57
9
A
ASP
52
71.33
112.02
9
A
ALA
53
-175.15
74.27
9
A
GLU
54
-39.24
111.70
9
A
ALA
55
-169.81
81.21
9
A
MET
57
-157.79
88.09
10
A
SER
3
62.60
140.15
10
A
SER
5
-150.57
-60.05
10
A
SER
6
60.70
161.87
10
A
THR
33
-93.89
42.42
10
A
ASN
35
40.59
73.23
10
A
ILE
44
-56.57
-70.13
10
A
ASP
50
60.94
103.71
10
A
ASP
52
-161.79
102.04
10
A
ALA
53
-158.85
74.64
10
A
ALA
55
-160.76
99.05
10
A
ALA
56
46.75
78.46
10
A
MET
57
-169.62
107.23
11
A
SER
3
-39.95
141.29
11
A
SER
5
53.28
83.40
11
A
SER
6
60.53
86.18
11
A
GLU
10
-90.40
-61.63
11
A
ILE
16
-54.71
-71.71
11
A
ASN
35
40.45
76.68
11
A
ILE
44
-63.93
-70.06
11
A
ASP
52
55.04
97.73
11
A
ALA
53
-156.04
-45.87
11
A
GLU
54
65.47
155.25
11
A
ALA
55
62.51
77.40
12
A
SER
5
-150.42
-61.47
12
A
SER
6
66.06
96.58
12
A
ASN
34
56.00
19.18
12
A
ASN
35
79.78
62.92
12
A
ILE
44
-71.01
-72.33
12
A
ASP
50
173.17
113.19
12
A
ASP
52
-124.53
-57.49
12
A
GLU
54
-156.80
-59.87
12
A
ALA
55
64.19
153.22
12
A
ALA
56
42.47
79.15
12
A
SER
61
-157.57
88.49
12
A
SER
62
57.64
83.93
13
A
SER
2
49.30
95.53
13
A
GLU
10
-90.16
-62.90
13
A
THR
33
-90.96
32.70
13
A
ASN
35
42.45
79.41
13
A
ILE
44
-56.10
-70.10
13
A
ASP
50
67.07
110.23
13
A
LEU
51
-104.17
-63.97
13
A
ALA
53
-161.77
-44.45
13
A
ALA
55
48.30
83.66
13
A
MET
57
56.99
109.65
13
A
SER
62
-175.02
126.54
14
A
SER
2
57.30
92.47
14
A
SER
3
57.89
96.07
14
A
ILE
16
-57.18
-71.35
14
A
THR
33
-93.79
42.42
14
A
ASP
50
-138.70
-47.25
14
A
ASP
52
42.70
86.83
14
A
GLU
54
68.79
148.63
14
A
ALA
55
-64.71
88.83
14
A
ALA
56
-166.40
62.05
15
A
SER
2
62.64
159.18
15
A
SER
3
-174.19
-58.50
15
A
ASN
34
44.12
73.12
15
A
ASN
35
40.47
83.44
15
A
ASP
50
-160.62
99.94
15
A
ASP
52
55.15
101.52
15
A
ALA
56
-173.88
102.24
15
A
SER
62
-43.55
107.80
16
A
SER
2
-162.06
110.22
16
A
SER
6
-142.39
-59.63
16
A
CYS
12
-50.24
-70.01
16
A
THR
33
-97.36
44.31
16
A
ILE
44
-64.80
-70.64
16
A
ASP
49
-100.01
69.82
16
A
ASP
50
-169.58
69.55
16
A
LEU
51
38.33
87.21
16
A
ASP
52
-171.67
92.37
16
A
GLU
54
-107.88
53.45
16
A
ALA
56
-58.14
171.83
16
A
SER
62
-170.65
82.49
17
A
SER
2
179.61
145.46
17
A
ASN
34
40.49
29.90
17
A
ASN
35
70.11
66.57
17
A
HIS
47
-90.79
45.47
17
A
ASP
49
70.26
-61.02
17
A
ASP
50
178.37
100.88
17
A
ASP
52
-152.02
-56.29
17
A
ALA
55
-133.17
-62.00
17
A
ALA
56
58.94
78.67
17
A
SER
62
63.13
106.92
18
A
ILE
16
-59.33
-72.41
18
A
THR
33
-95.51
43.03
18
A
ASN
35
67.89
71.10
18
A
ILE
44
-62.67
-71.26
18
A
LEU
51
-102.29
69.30
18
A
ASP
52
-179.06
128.36
18
A
GLU
54
48.75
97.30
18
A
ALA
56
63.18
106.31
19
A
SER
3
67.17
-72.34
19
A
SER
6
65.94
153.06
19
A
THR
33
-89.81
39.39
19
A
ASN
35
67.72
70.55
19
A
HIS
47
-91.58
43.76
19
A
ASP
52
44.66
91.27
20
A
SER
3
-176.50
128.74
20
A
SER
5
64.38
88.61
20
A
SER
6
-155.70
-58.63
20
A
THR
33
-96.21
43.61
20
A
ASN
35
40.21
70.71
20
A
LEU
51
38.36
78.82
20
A
ASP
52
174.44
118.90
20
A
ALA
55
61.66
168.82
Solution Structure of the Second UBA Domain in the Human Ubiquitin Specific Protease 5 (Isopeptidase 5)
1
N
N
A
PRO
9
A
PRO
9
HELX_P
A
GLY
20
A
GLY
20
1
1
12
A
SER
22
A
SER
22
HELX_P
A
THR
33
A
THR
33
1
2
12
A
LEU
37
A
LEU
37
HELX_P
A
ASP
50
A
ASP
50
1
3
14
HYDROLASE
isopeptidase T, Ubiquitin Specific Protease 5, USP 5, UBA domain, structural genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, HYDROLASE
UBP5_HUMAN
UNP
1
723
P45974
723
772
2DAK
8
57
P45974
A
1
8
57
1
cloning artifact
GLY
1
2DAK
A
P45974
UNP
1
1
cloning artifact
SER
2
2DAK
A
P45974
UNP
2
1
cloning artifact
SER
3
2DAK
A
P45974
UNP
3
1
cloning artifact
GLY
4
2DAK
A
P45974
UNP
4
1
cloning artifact
SER
5
2DAK
A
P45974
UNP
5
1
cloning artifact
SER
6
2DAK
A
P45974
UNP
6
1
cloning artifact
GLY
7
2DAK
A
P45974
UNP
7
1
cloning artifact
SER
58
2DAK
A
P45974
UNP
58
1
cloning artifact
GLY
59
2DAK
A
P45974
UNP
59
1
cloning artifact
PRO
60
2DAK
A
P45974
UNP
60
1
cloning artifact
SER
61
2DAK
A
P45974
UNP
61
1
cloning artifact
SER
62
2DAK
A
P45974
UNP
62
1
cloning artifact
GLY
63
2DAK
A
P45974
UNP
63