1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Niraula, T.N.
Tomizawa, T.
Koshiba, K.
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
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 Second PDZ domain of PDZ Domain Containing Protein 1
10.2210/pdb2eei/pdb
pdb_00002eei
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
11357.752
PDZ domain-containing protein 1
pdz domain
1
man
polymer
CFTR-associated protein of 70 kDa, Na/Pi cotransporter C-terminal-associated protein, NaPi-Cap1, Na(+)/H(+) exchanger regulatory factor 3, Sodium-hydrogen exchanger regulatory factor 3
no
no
GSSGSSGQPRLCYLVKEGGSYGFSLKTVQGKKGVYMTDITPQGVAMRAGVLADDHLIEVNGENVEDASHEEVVEKVKKSG
SRVMFLLVDKETDKRHVEQKSGPSSG
GSSGSSGQPRLCYLVKEGGSYGFSLKTVQGKKGVYMTDITPQGVAMRAGVLADDHLIEVNGENVEDASHEEVVEKVKKSG
SRVMFLLVDKETDKRHVEQKSGPSSG
A
hss001001614.1
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
human
Homo
sample
Cell-free protein synthesis
PDZK1
9606
Homo sapiens
Plasmid
P050905-17
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
Data collection
Database references
Derived calculations
1
0
2008-02-26
1
1
2011-07-13
1
2
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
Different domain of the same protein
Y
PDBJ
Y
PDBJ
2007-02-15
REL
REL
structures with the least restraint violations, target function
100
20
3D_15N-separated_NOESY
3D_13C-separated_NOESY
120mM
7.0
ambient
298
K
torsion angle dynamics
1
lowest energy
3.36mM PDZ domain U-13C,15N; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D20, 90% H2O
10% D20, 90% H2O
Bruker
collection
XwinNMR
3.5
Delaglio, F.
processing
NMRPipe
20031121
Johnson, B.A.
data analysis
NMRView
5.0.4
Kobayashi, N.
data analysis
KUJIRA
0.9820
Guntert, P.
structure solution
CYANA
2.0.17
Guntert, P.
refinement
CYANA
2.0.17
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
GLN
8
n
8
GLN
8
A
PRO
9
n
9
PRO
9
A
ARG
10
n
10
ARG
10
A
LEU
11
n
11
LEU
11
A
CYS
12
n
12
CYS
12
A
TYR
13
n
13
TYR
13
A
LEU
14
n
14
LEU
14
A
VAL
15
n
15
VAL
15
A
LYS
16
n
16
LYS
16
A
GLU
17
n
17
GLU
17
A
GLY
18
n
18
GLY
18
A
GLY
19
n
19
GLY
19
A
SER
20
n
20
SER
20
A
TYR
21
n
21
TYR
21
A
GLY
22
n
22
GLY
22
A
PHE
23
n
23
PHE
23
A
SER
24
n
24
SER
24
A
LEU
25
n
25
LEU
25
A
LYS
26
n
26
LYS
26
A
THR
27
n
27
THR
27
A
VAL
28
n
28
VAL
28
A
GLN
29
n
29
GLN
29
A
GLY
30
n
30
GLY
30
A
LYS
31
n
31
LYS
31
A
LYS
32
n
32
LYS
32
A
GLY
33
n
33
GLY
33
A
VAL
34
n
34
VAL
34
A
TYR
35
n
35
TYR
35
A
MET
36
n
36
MET
36
A
THR
37
n
37
THR
37
A
ASP
38
n
38
ASP
38
A
ILE
39
n
39
ILE
39
A
THR
40
n
40
THR
40
A
PRO
41
n
41
PRO
41
A
GLN
42
n
42
GLN
42
A
GLY
43
n
43
GLY
43
A
VAL
44
n
44
VAL
44
A
ALA
45
n
45
ALA
45
A
MET
46
n
46
MET
46
A
ARG
47
n
47
ARG
47
A
ALA
48
n
48
ALA
48
A
GLY
49
n
49
GLY
49
A
VAL
50
n
50
VAL
50
A
LEU
51
n
51
LEU
51
A
ALA
52
n
52
ALA
52
A
ASP
53
n
53
ASP
53
A
ASP
54
n
54
ASP
54
A
HIS
55
n
55
HIS
55
A
LEU
56
n
56
LEU
56
A
ILE
57
n
57
ILE
57
A
GLU
58
n
58
GLU
58
A
VAL
59
n
59
VAL
59
A
ASN
60
n
60
ASN
60
A
GLY
61
n
61
GLY
61
A
GLU
62
n
62
GLU
62
A
ASN
63
n
63
ASN
63
A
VAL
64
n
64
VAL
64
A
GLU
65
n
65
GLU
65
A
ASP
66
n
66
ASP
66
A
ALA
67
n
67
ALA
67
A
SER
68
n
68
SER
68
A
HIS
69
n
69
HIS
69
A
GLU
70
n
70
GLU
70
A
GLU
71
n
71
GLU
71
A
VAL
72
n
72
VAL
72
A
VAL
73
n
73
VAL
73
A
GLU
74
n
74
GLU
74
A
LYS
75
n
75
LYS
75
A
VAL
76
n
76
VAL
76
A
LYS
77
n
77
LYS
77
A
LYS
78
n
78
LYS
78
A
SER
79
n
79
SER
79
A
GLY
80
n
80
GLY
80
A
SER
81
n
81
SER
81
A
ARG
82
n
82
ARG
82
A
VAL
83
n
83
VAL
83
A
MET
84
n
84
MET
84
A
PHE
85
n
85
PHE
85
A
LEU
86
n
86
LEU
86
A
LEU
87
n
87
LEU
87
A
VAL
88
n
88
VAL
88
A
ASP
89
n
89
ASP
89
A
LYS
90
n
90
LYS
90
A
GLU
91
n
91
GLU
91
A
THR
92
n
92
THR
92
A
ASP
93
n
93
ASP
93
A
LYS
94
n
94
LYS
94
A
ARG
95
n
95
ARG
95
A
HIS
96
n
96
HIS
96
A
VAL
97
n
97
VAL
97
A
GLU
98
n
98
GLU
98
A
GLN
99
n
99
GLN
99
A
LYS
100
n
100
LYS
100
A
SER
101
n
101
SER
101
A
GLY
102
n
102
GLY
102
A
PRO
103
n
103
PRO
103
A
SER
104
n
104
SER
104
A
SER
105
n
105
SER
105
A
GLY
106
n
106
GLY
106
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
CYS
12
A
N
CYS
12
A
O
PHE
85
A
O
PHE
85
A
O
LEU
86
A
O
LEU
86
A
N
ILE
57
A
N
ILE
57
A
O
ASP
54
A
O
ASP
54
A
N
MET
36
A
N
MET
36
A
O
TYR
35
A
O
TYR
35
A
N
LYS
26
A
N
LYS
26
A
N
CYS
12
A
N
CYS
12
A
O
PHE
85
A
O
PHE
85
A
O
LEU
86
A
O
LEU
86
A
N
ILE
57
A
N
ILE
57
A
N
VAL
59
A
N
VAL
59
A
O
GLU
62
A
O
GLU
62
1
A
GLU
17
-131.80
-56.97
1
A
TYR
21
-50.21
176.48
1
A
GLN
42
34.41
43.64
1
A
GLU
58
-173.84
145.07
1
A
ASN
60
47.51
29.17
1
A
SER
79
-36.22
-39.11
1
A
HIS
96
-64.33
95.99
1
A
GLN
99
-51.26
88.92
2
A
GLU
17
-121.69
-57.21
2
A
TYR
21
-42.92
-73.15
2
A
PHE
23
-56.55
176.11
2
A
GLN
29
-82.05
41.87
2
A
THR
40
-37.86
127.52
2
A
ASP
53
39.86
28.06
2
A
LYS
94
-82.12
41.33
2
A
SER
105
-127.17
-52.54
3
A
LYS
16
-49.51
104.17
3
A
GLU
17
-101.70
-63.33
3
A
TYR
21
-48.96
167.08
3
A
HIS
55
-54.67
102.61
3
A
VAL
73
-39.69
-31.28
3
A
ARG
95
-69.48
95.17
4
A
LYS
16
-62.47
85.81
4
A
SER
20
-105.93
-68.77
4
A
THR
40
-33.74
135.93
4
A
GLN
42
33.85
40.50
4
A
ASN
63
-55.77
105.43
4
A
SER
81
-121.28
-52.07
4
A
ASP
93
-35.28
118.31
5
A
SER
6
-95.51
-63.09
5
A
PRO
9
-69.83
-168.90
5
A
TYR
21
-52.14
174.16
5
A
LYS
31
-68.85
-177.03
5
A
ASP
53
38.89
31.28
5
A
HIS
55
-52.13
108.73
5
A
ASN
63
-54.18
101.39
5
A
VAL
73
-37.01
-34.86
5
A
ARG
95
-65.94
91.25
5
A
SER
105
-97.03
-61.66
6
A
PRO
9
-69.76
-168.49
6
A
LYS
16
-44.35
106.66
6
A
GLU
17
-103.25
-62.07
6
A
TYR
21
-53.92
-175.69
6
A
ALA
45
-71.39
-72.99
6
A
ASP
53
47.24
29.24
6
A
VAL
73
-35.16
-35.64
6
A
ARG
95
-174.82
130.94
6
A
HIS
96
-81.20
45.77
6
A
SER
101
-34.65
98.68
6
A
PRO
103
-69.74
2.76
6
A
SER
104
72.45
40.94
7
A
LYS
16
-61.92
99.13
7
A
GLU
17
-99.76
-60.78
7
A
TYR
21
-66.14
-72.17
7
A
THR
40
-38.44
137.69
7
A
GLN
42
36.07
37.29
7
A
HIS
55
-52.60
100.76
7
A
SER
81
-132.50
-37.34
7
A
LYS
94
-58.95
89.66
7
A
HIS
96
-47.39
101.38
7
A
VAL
97
-36.19
125.25
8
A
PRO
9
-69.73
-176.74
8
A
GLU
17
-122.03
-64.18
8
A
TYR
21
-68.26
-71.97
8
A
GLN
42
34.15
46.73
8
A
GLU
58
-173.30
144.53
8
A
ASN
60
38.05
34.77
8
A
VAL
73
-38.43
-35.09
8
A
LYS
94
-41.74
105.97
8
A
SER
101
-102.67
-62.58
8
A
SER
104
-58.25
99.06
9
A
LYS
16
-51.43
95.35
9
A
TYR
21
-38.57
-70.13
9
A
GLN
42
70.30
35.75
9
A
GLU
58
-170.12
142.42
9
A
ASN
63
-35.45
122.59
9
A
SER
79
-35.11
-38.40
9
A
GLN
99
-53.26
177.11
10
A
SER
3
-35.08
116.56
10
A
PRO
9
-69.78
-179.17
10
A
LYS
16
-47.62
105.03
10
A
TYR
21
-47.58
172.98
10
A
HIS
55
-51.62
103.23
10
A
HIS
96
-67.30
87.75
10
A
PRO
103
-69.70
1.79
10
A
SER
104
-35.86
121.12
11
A
SER
2
-85.93
48.16
11
A
SER
5
-93.03
40.51
11
A
LYS
16
-45.29
105.72
11
A
THR
40
-34.33
131.84
11
A
ASP
53
47.57
26.44
11
A
SER
105
37.90
47.02
12
A
ASN
63
-50.37
107.11
12
A
SER
104
-120.58
-57.53
12
A
SER
105
-59.22
107.64
13
A
TYR
21
-44.05
-74.03
13
A
LYS
31
-58.47
-177.43
13
A
GLN
42
71.22
50.67
13
A
ALA
45
-73.08
-70.03
13
A
ASN
63
-58.75
109.45
14
A
PRO
9
-69.74
-175.15
14
A
LYS
16
-59.17
93.35
14
A
HIS
55
-50.59
100.49
14
A
ASN
63
-58.80
109.30
14
A
VAL
73
-38.90
-38.10
14
A
GLN
99
-171.56
139.66
14
A
SER
105
34.36
43.09
15
A
GLU
17
-123.46
-73.48
15
A
TYR
21
-66.88
-174.56
15
A
THR
37
-120.13
-50.67
15
A
THR
40
-34.17
137.26
15
A
HIS
55
-57.97
109.35
15
A
ASN
63
-47.33
105.98
15
A
SER
104
-36.43
108.91
16
A
SER
3
-34.77
123.58
16
A
PRO
9
-69.79
-170.60
16
A
TYR
21
-68.89
-175.49
16
A
VAL
44
-54.16
-71.19
16
A
ASN
60
36.94
30.29
16
A
ASP
66
-108.89
40.04
17
A
SER
3
-171.17
144.82
17
A
GLU
17
-120.64
-60.55
17
A
SER
79
-35.12
-38.78
17
A
ASP
93
-34.58
128.52
17
A
SER
101
-53.70
106.53
18
A
SER
3
-52.92
106.04
18
A
PRO
9
-69.79
-179.56
18
A
LYS
16
-56.59
100.09
18
A
TYR
21
-46.64
173.20
18
A
GLU
58
-175.57
142.58
18
A
GLN
99
42.43
28.48
19
A
PRO
9
-69.76
-171.37
19
A
LYS
16
-44.18
106.58
19
A
TYR
21
-51.35
172.26
19
A
LYS
31
-60.80
-179.12
19
A
ALA
52
-46.77
158.98
19
A
HIS
55
-53.49
108.92
20
A
SER
5
-170.88
125.46
20
A
TYR
21
-51.37
-73.86
20
A
ALA
45
-63.75
-71.67
20
A
ASP
53
73.65
44.56
20
A
ASN
60
48.48
27.51
20
A
GLU
62
-162.86
114.99
20
A
ASP
93
-81.93
39.16
20
A
LYS
94
33.51
45.48
20
A
PRO
103
-69.78
2.72
20
A
SER
104
-34.53
99.99
Solution Structure of Second PDZ domain of PDZ Domain Containing Protein 1
1
N
N
A
GLY
43
A
GLY
43
HELX_P
A
GLY
49
A
GLY
49
1
1
7
A
SER
68
A
SER
68
HELX_P
A
GLY
80
A
GLY
80
1
2
13
METAL BINDING PROTEIN
PDZ domain, regulatory factor, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, METAL BINDING PROTEIN
PDZD1_HUMAN
UNP
1
132
Q5T2W1
QPRLCYLVKEGGSYGFSLKTVQGKKGVYMTDITPQGVAMRAGVLADDHLIEVNGENVEDASHEEVVEKVKKSGSRVMFLL
VDKETDKRHVEQK
132
224
2EEI
8
100
Q5T2W1
A
1
8
100
1
expression tag
GLY
1
2EEI
A
Q5T2W1
UNP
1
1
expression tag
SER
2
2EEI
A
Q5T2W1
UNP
2
1
expression tag
SER
3
2EEI
A
Q5T2W1
UNP
3
1
expression tag
GLY
4
2EEI
A
Q5T2W1
UNP
4
1
expression tag
SER
5
2EEI
A
Q5T2W1
UNP
5
1
expression tag
SER
6
2EEI
A
Q5T2W1
UNP
6
1
expression tag
GLY
7
2EEI
A
Q5T2W1
UNP
7
1
expression tag
SER
101
2EEI
A
Q5T2W1
UNP
101
1
expression tag
GLY
102
2EEI
A
Q5T2W1
UNP
102
1
expression tag
PRO
103
2EEI
A
Q5T2W1
UNP
103
1
expression tag
SER
104
2EEI
A
Q5T2W1
UNP
104
1
expression tag
SER
105
2EEI
A
Q5T2W1
UNP
105
1
expression tag
GLY
106
2EEI
A
Q5T2W1
UNP
106
5
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ARG
10
A
ARG
10
A
VAL
15
A
VAL
15
A
ARG
82
A
ARG
82
A
LEU
87
A
LEU
87
A
ASP
54
A
ASP
54
A
VAL
59
A
VAL
59
A
TYR
35
A
TYR
35
A
MET
36
A
MET
36
A
LEU
25
A
LEU
25
A
LYS
26
A
LYS
26
A
ARG
10
A
ARG
10
A
VAL
15
A
VAL
15
A
ARG
82
A
ARG
82
A
LEU
87
A
LEU
87
A
ASP
54
A
ASP
54
A
VAL
59
A
VAL
59
A
GLU
62
A
GLU
62
A
ASN
63
A
ASN
63