1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Tochio, N.
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 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
To be Published
0353
The solution structure of the second thioredoxin-like domain of human Protein disulfide-isomerase
10.2210/pdb1x5c/pdb
pdb_00001x5c
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
13251.812
Protein disulfide-isomerase
5.3.4.1
Thioredoxin like domain
1
man
polymer
PDI, Prolyl 4- hydroxylase beta subunit, Cellular thyroid hormone binding protein, p55
no
no
GSSGSSGPVKVLVGKNFEDVAFDEKKNVFVEFYAPWCGHCKQLAPIWDKLGETYKDHENIVIAKMDSTANEVEAVKVHSF
PTLKFFPASADRTVIDYNGERTLDGFKKFLESGGQSGPSSG
GSSGSSGPVKVLVGKNFEDVAFDEKKNVFVEFYAPWCGHCKQLAPIWDKLGETYKDHENIVIAKMDSTANEVEAVKVHSF
PTLKFFPASADRTVIDYNGERTLDGFKKFLESGGQSGPSSG
A
hss001002456.1
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
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
P4HB
9606
Homo sapiens
PLASMID
P040628-09
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
2005-11-15
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
2005-05-15
REL
REL
target function,structures with the least restraint violations
100
20
3D_15N-separated_NOESY
3D_13C-separated_NOESY
120mM
7.0
ambient
296
K
torsion angle dynamics
1
lowest energy
1.2mM thioredoxin like domain U-15N,13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 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
0.9044
Guntert, P.
structure solution
CYANA
2.0.17
Guntert, P.
refinement
CYANA
2.0.17
900
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
VAL
9
n
9
VAL
9
A
LYS
10
n
10
LYS
10
A
VAL
11
n
11
VAL
11
A
LEU
12
n
12
LEU
12
A
VAL
13
n
13
VAL
13
A
GLY
14
n
14
GLY
14
A
LYS
15
n
15
LYS
15
A
ASN
16
n
16
ASN
16
A
PHE
17
n
17
PHE
17
A
GLU
18
n
18
GLU
18
A
ASP
19
n
19
ASP
19
A
VAL
20
n
20
VAL
20
A
ALA
21
n
21
ALA
21
A
PHE
22
n
22
PHE
22
A
ASP
23
n
23
ASP
23
A
GLU
24
n
24
GLU
24
A
LYS
25
n
25
LYS
25
A
LYS
26
n
26
LYS
26
A
ASN
27
n
27
ASN
27
A
VAL
28
n
28
VAL
28
A
PHE
29
n
29
PHE
29
A
VAL
30
n
30
VAL
30
A
GLU
31
n
31
GLU
31
A
PHE
32
n
32
PHE
32
A
TYR
33
n
33
TYR
33
A
ALA
34
n
34
ALA
34
A
PRO
35
n
35
PRO
35
A
TRP
36
n
36
TRP
36
A
CYS
37
n
37
CYS
37
A
GLY
38
n
38
GLY
38
A
HIS
39
n
39
HIS
39
A
CYS
40
n
40
CYS
40
A
LYS
41
n
41
LYS
41
A
GLN
42
n
42
GLN
42
A
LEU
43
n
43
LEU
43
A
ALA
44
n
44
ALA
44
A
PRO
45
n
45
PRO
45
A
ILE
46
n
46
ILE
46
A
TRP
47
n
47
TRP
47
A
ASP
48
n
48
ASP
48
A
LYS
49
n
49
LYS
49
A
LEU
50
n
50
LEU
50
A
GLY
51
n
51
GLY
51
A
GLU
52
n
52
GLU
52
A
THR
53
n
53
THR
53
A
TYR
54
n
54
TYR
54
A
LYS
55
n
55
LYS
55
A
ASP
56
n
56
ASP
56
A
HIS
57
n
57
HIS
57
A
GLU
58
n
58
GLU
58
A
ASN
59
n
59
ASN
59
A
ILE
60
n
60
ILE
60
A
VAL
61
n
61
VAL
61
A
ILE
62
n
62
ILE
62
A
ALA
63
n
63
ALA
63
A
LYS
64
n
64
LYS
64
A
MET
65
n
65
MET
65
A
ASP
66
n
66
ASP
66
A
SER
67
n
67
SER
67
A
THR
68
n
68
THR
68
A
ALA
69
n
69
ALA
69
A
ASN
70
n
70
ASN
70
A
GLU
71
n
71
GLU
71
A
VAL
72
n
72
VAL
72
A
GLU
73
n
73
GLU
73
A
ALA
74
n
74
ALA
74
A
VAL
75
n
75
VAL
75
A
LYS
76
n
76
LYS
76
A
VAL
77
n
77
VAL
77
A
HIS
78
n
78
HIS
78
A
SER
79
n
79
SER
79
A
PHE
80
n
80
PHE
80
A
PRO
81
n
81
PRO
81
A
THR
82
n
82
THR
82
A
LEU
83
n
83
LEU
83
A
LYS
84
n
84
LYS
84
A
PHE
85
n
85
PHE
85
A
PHE
86
n
86
PHE
86
A
PRO
87
n
87
PRO
87
A
ALA
88
n
88
ALA
88
A
SER
89
n
89
SER
89
A
ALA
90
n
90
ALA
90
A
ASP
91
n
91
ASP
91
A
ARG
92
n
92
ARG
92
A
THR
93
n
93
THR
93
A
VAL
94
n
94
VAL
94
A
ILE
95
n
95
ILE
95
A
ASP
96
n
96
ASP
96
A
TYR
97
n
97
TYR
97
A
ASN
98
n
98
ASN
98
A
GLY
99
n
99
GLY
99
A
GLU
100
n
100
GLU
100
A
ARG
101
n
101
ARG
101
A
THR
102
n
102
THR
102
A
LEU
103
n
103
LEU
103
A
ASP
104
n
104
ASP
104
A
GLY
105
n
105
GLY
105
A
PHE
106
n
106
PHE
106
A
LYS
107
n
107
LYS
107
A
LYS
108
n
108
LYS
108
A
PHE
109
n
109
PHE
109
A
LEU
110
n
110
LEU
110
A
GLU
111
n
111
GLU
111
A
SER
112
n
112
SER
112
A
GLY
113
n
113
GLY
113
A
GLY
114
n
114
GLY
114
A
GLN
115
n
115
GLN
115
A
SER
116
n
116
SER
116
A
GLY
117
n
117
GLY
117
A
PRO
118
n
118
PRO
118
A
SER
119
n
119
SER
119
A
SER
120
n
120
SER
120
A
GLY
121
n
121
GLY
121
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
N
LYS
10
A
N
LYS
10
A
O
LYS
64
A
O
LYS
64
A
O
VAL
61
A
O
VAL
61
A
N
ASN
27
A
N
ASN
27
A
N
PHE
32
A
N
PHE
32
A
O
THR
82
A
O
THR
82
A
N
PHE
85
A
N
PHE
85
A
O
ILE
95
A
O
ILE
95
1
A
SER
3
-161.78
108.36
1
A
SER
5
-130.22
-48.13
1
A
SER
6
-41.36
159.78
1
A
HIS
57
-66.95
-175.39
1
A
ALA
88
-63.41
74.70
1
A
ARG
92
-92.10
37.40
1
A
ASN
98
-112.69
50.10
1
A
GLU
111
-38.72
-35.90
2
A
SER
5
-96.77
43.31
2
A
HIS
39
-39.28
-33.92
2
A
HIS
57
-66.89
-176.31
2
A
ALA
88
-83.14
40.45
2
A
ARG
92
-93.79
49.75
2
A
GLU
111
-38.94
-37.91
3
A
CYS
37
-57.21
109.44
3
A
HIS
57
-66.26
-174.81
3
A
ARG
92
34.34
46.42
3
A
GLU
111
-36.53
-38.82
3
A
SER
120
-134.47
-57.86
4
A
SER
2
-61.56
89.32
4
A
SER
5
-101.69
44.85
4
A
ALA
21
-92.28
-63.75
4
A
CYS
37
-58.66
103.70
4
A
HIS
57
-65.01
-175.02
4
A
SER
89
-35.28
140.64
4
A
ARG
92
-85.63
40.00
4
A
GLU
111
-38.01
-38.83
5
A
HIS
57
-66.11
-174.71
5
A
ALA
88
-77.96
47.29
5
A
GLU
111
-37.35
-37.94
5
A
SER
119
-35.49
113.43
6
A
SER
6
-64.91
96.53
6
A
HIS
57
-68.24
-174.36
6
A
ARG
101
74.50
46.45
6
A
GLU
111
-36.57
-36.58
6
A
PRO
118
-69.75
2.84
7
A
HIS
57
-65.84
-173.52
7
A
ARG
92
34.30
42.35
7
A
GLU
111
-38.35
-37.97
7
A
SER
120
-95.89
41.75
8
A
SER
6
-38.82
-38.45
8
A
HIS
57
-64.48
-174.74
8
A
ARG
92
31.98
53.46
8
A
GLU
111
-37.36
-36.53
8
A
SER
119
-121.91
-55.78
9
A
HIS
39
-39.35
-38.31
9
A
HIS
57
-66.00
-174.88
9
A
ASP
91
-90.95
34.61
9
A
ARG
92
35.94
42.81
9
A
ARG
101
74.43
45.84
9
A
GLU
111
-36.59
-38.71
9
A
PRO
118
-69.81
4.95
10
A
HIS
57
-67.53
-175.99
10
A
ARG
92
37.14
47.25
10
A
SER
116
-175.18
134.18
10
A
SER
119
-48.89
155.11
11
A
SER
2
-116.50
50.86
11
A
HIS
57
-64.29
-174.68
11
A
ALA
88
-75.75
48.91
11
A
ASP
91
-99.66
38.95
11
A
ARG
92
36.20
38.56
11
A
SER
116
-173.00
129.46
12
A
SER
2
-58.04
97.77
12
A
HIS
57
-68.96
-174.54
12
A
ASP
91
-84.70
34.77
12
A
ARG
92
34.06
48.94
12
A
GLU
111
-37.86
-38.76
12
A
SER
116
-107.02
-60.95
12
A
SER
119
-125.38
-55.80
12
A
SER
120
38.44
42.01
13
A
SER
5
-170.04
140.57
13
A
HIS
57
-67.90
-174.42
13
A
ALA
88
-66.97
84.45
13
A
ALA
90
-49.13
-18.56
13
A
GLU
111
-37.61
-34.90
14
A
CYS
37
-60.00
106.50
14
A
HIS
57
-66.80
-175.04
14
A
ARG
92
28.57
47.82
14
A
ARG
101
73.21
44.08
15
A
SER
6
-91.53
43.99
15
A
HIS
57
-62.21
-174.33
15
A
ASP
91
-91.90
32.49
15
A
ARG
92
33.25
39.89
16
A
HIS
57
-67.98
-176.26
16
A
ALA
88
-78.62
48.38
16
A
ALA
90
-86.80
31.07
16
A
SER
119
-47.13
155.67
17
A
HIS
57
-64.12
-175.20
17
A
ARG
92
35.38
35.70
18
A
HIS
57
-64.15
-175.08
18
A
ALA
88
-62.03
80.36
18
A
ARG
92
35.42
54.52
18
A
ASN
98
-118.71
51.38
18
A
GLU
111
-38.25
-39.26
18
A
PRO
118
-69.69
98.67
19
A
ALA
21
-91.72
-63.83
19
A
HIS
57
-63.99
-175.61
19
A
ARG
92
-98.76
40.21
19
A
GLN
115
-52.11
108.32
20
A
PHE
22
-81.96
48.68
20
A
LYS
25
48.87
28.62
20
A
HIS
57
-63.50
-175.82
20
A
ALA
88
-81.78
42.24
20
A
ARG
92
35.33
50.57
20
A
PRO
118
-69.79
80.94
20
A
SER
120
37.71
40.73
The solution structure of the second thioredoxin-like domain of human Protein disulfide-isomerase
1
N
N
A
ASN
16
A
ASN
16
HELX_P
A
ALA
21
A
ALA
21
1
1
6
A
CYS
37
A
CYS
37
HELX_P
A
GLU
52
A
GLU
52
1
2
16
A
THR
53
A
THR
53
HELX_P
A
LYS
55
A
LYS
55
5
3
3
A
THR
102
A
THR
102
HELX_P
A
GLY
113
A
GLY
113
1
4
12
ISOMERASE
DSI, ERBA2L, GIT, PDI, PDIA1, PO4DB, PO4HB, PROHB, thioredoxin like domain, redox, structural genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, ISOMERASE
A
PHE
80
A
PHE
80
1
A
PRO
81
A
PRO
81
0.03
A
PHE
80
A
PHE
80
2
A
PRO
81
A
PRO
81
0.03
A
PHE
80
A
PHE
80
3
A
PRO
81
A
PRO
81
-0.04
A
PHE
80
A
PHE
80
4
A
PRO
81
A
PRO
81
0.02
A
PHE
80
A
PHE
80
5
A
PRO
81
A
PRO
81
0.07
A
PHE
80
A
PHE
80
6
A
PRO
81
A
PRO
81
0.03
A
PHE
80
A
PHE
80
7
A
PRO
81
A
PRO
81
0.06
A
PHE
80
A
PHE
80
8
A
PRO
81
A
PRO
81
-0.04
A
PHE
80
A
PHE
80
9
A
PRO
81
A
PRO
81
0.02
A
PHE
80
A
PHE
80
10
A
PRO
81
A
PRO
81
0.03
A
PHE
80
A
PHE
80
11
A
PRO
81
A
PRO
81
0.00
A
PHE
80
A
PHE
80
12
A
PRO
81
A
PRO
81
0.00
A
PHE
80
A
PHE
80
13
A
PRO
81
A
PRO
81
0.07
A
PHE
80
A
PHE
80
14
A
PRO
81
A
PRO
81
0.04
A
PHE
80
A
PHE
80
15
A
PRO
81
A
PRO
81
-0.03
A
PHE
80
A
PHE
80
16
A
PRO
81
A
PRO
81
0.04
A
PHE
80
A
PHE
80
17
A
PRO
81
A
PRO
81
0.01
A
PHE
80
A
PHE
80
18
A
PRO
81
A
PRO
81
0.02
A
PHE
80
A
PHE
80
19
A
PRO
81
A
PRO
81
0.04
A
PHE
80
A
PHE
80
20
A
PRO
81
A
PRO
81
0.01
PDIA1_HUMAN
UNP
1
368
P07237
PVKVLVGKNFEDVAFDEKKNVFVEFYAPWCGHCKQLAPIWDKLGETYKDHENIVIAKMDSTANEVEAVKVHSFPTLKFFP
ASADRTVIDYNGERTLDGFKKFLESGGQ
368
475
1X5C
8
115
P07237
A
1
8
115
1
cloning artifact
GLY
1
1X5C
A
P07237
UNP
1
1
cloning artifact
SER
2
1X5C
A
P07237
UNP
2
1
cloning artifact
SER
3
1X5C
A
P07237
UNP
3
1
cloning artifact
GLY
4
1X5C
A
P07237
UNP
4
1
cloning artifact
SER
5
1X5C
A
P07237
UNP
5
1
cloning artifact
SER
6
1X5C
A
P07237
UNP
6
1
cloning artifact
GLY
7
1X5C
A
P07237
UNP
7
1
cloning artifact
SER
116
1X5C
A
P07237
UNP
116
1
cloning artifact
GLY
117
1X5C
A
P07237
UNP
117
1
cloning artifact
PRO
118
1X5C
A
P07237
UNP
118
1
cloning artifact
SER
119
1X5C
A
P07237
UNP
119
1
cloning artifact
SER
120
1X5C
A
P07237
UNP
120
1
cloning artifact
GLY
121
1X5C
A
P07237
UNP
121
5
parallel
parallel
anti-parallel
anti-parallel
A
LYS
10
A
LYS
10
A
LEU
12
A
LEU
12
A
ILE
60
A
ILE
60
A
ASP
66
A
ASP
66
A
ASN
27
A
ASN
27
A
TYR
33
A
TYR
33
A
THR
82
A
THR
82
A
PHE
86
A
PHE
86
A
ILE
95
A
ILE
95
A
ASP
96
A
ASP
96