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
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 PDZ domain of PDZ and LIM domain protein
10.2210/pdb2eeg/pdb
pdb_00002eeg
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
9604.780
PDZ and LIM domain protein 4
PDZ domain
1
man
polymer
LIM protein RIL, Reversion-induced LIM protein
no
no
GSSGSSGMPHSVTLRGPSPWGFRLVGGRDFSAPLTISRVHAGSKAALAALCPGDLIQAINGESTELMTHLEAQNRIKGCH
DHLTLSVSSGPSSG
GSSGSSGMPHSVTLRGPSPWGFRLVGGRDFSAPLTISRVHAGSKAALAALCPGDLIQAINGESTELMTHLEAQNRIKGCH
DHLTLSVSSGPSSG
A
hsi002004534.1
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
human
Homo
sample
Cell-free protein synthesis
PDLIM4
9606
Homo sapiens
Plasmid
P050627-04
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
2007-08-21
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
Y
PDBJ
Y
PDBJ
2007-02-15
REL
REL
structures with the least restraint violations, target function
100
20
3D_13C-separated_NOESY
3D_15N-separated_NOESY
120mM
7.0
ambient
296
K
torsion angle dynamics
1
lowest energy
2.64mM 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
2.6
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
MET
8
n
8
MET
8
A
PRO
9
n
9
PRO
9
A
HIS
10
n
10
HIS
10
A
SER
11
n
11
SER
11
A
VAL
12
n
12
VAL
12
A
THR
13
n
13
THR
13
A
LEU
14
n
14
LEU
14
A
ARG
15
n
15
ARG
15
A
GLY
16
n
16
GLY
16
A
PRO
17
n
17
PRO
17
A
SER
18
n
18
SER
18
A
PRO
19
n
19
PRO
19
A
TRP
20
n
20
TRP
20
A
GLY
21
n
21
GLY
21
A
PHE
22
n
22
PHE
22
A
ARG
23
n
23
ARG
23
A
LEU
24
n
24
LEU
24
A
VAL
25
n
25
VAL
25
A
GLY
26
n
26
GLY
26
A
GLY
27
n
27
GLY
27
A
ARG
28
n
28
ARG
28
A
ASP
29
n
29
ASP
29
A
PHE
30
n
30
PHE
30
A
SER
31
n
31
SER
31
A
ALA
32
n
32
ALA
32
A
PRO
33
n
33
PRO
33
A
LEU
34
n
34
LEU
34
A
THR
35
n
35
THR
35
A
ILE
36
n
36
ILE
36
A
SER
37
n
37
SER
37
A
ARG
38
n
38
ARG
38
A
VAL
39
n
39
VAL
39
A
HIS
40
n
40
HIS
40
A
ALA
41
n
41
ALA
41
A
GLY
42
n
42
GLY
42
A
SER
43
n
43
SER
43
A
LYS
44
n
44
LYS
44
A
ALA
45
n
45
ALA
45
A
ALA
46
n
46
ALA
46
A
LEU
47
n
47
LEU
47
A
ALA
48
n
48
ALA
48
A
ALA
49
n
49
ALA
49
A
LEU
50
n
50
LEU
50
A
CYS
51
n
51
CYS
51
A
PRO
52
n
52
PRO
52
A
GLY
53
n
53
GLY
53
A
ASP
54
n
54
ASP
54
A
LEU
55
n
55
LEU
55
A
ILE
56
n
56
ILE
56
A
GLN
57
n
57
GLN
57
A
ALA
58
n
58
ALA
58
A
ILE
59
n
59
ILE
59
A
ASN
60
n
60
ASN
60
A
GLY
61
n
61
GLY
61
A
GLU
62
n
62
GLU
62
A
SER
63
n
63
SER
63
A
THR
64
n
64
THR
64
A
GLU
65
n
65
GLU
65
A
LEU
66
n
66
LEU
66
A
MET
67
n
67
MET
67
A
THR
68
n
68
THR
68
A
HIS
69
n
69
HIS
69
A
LEU
70
n
70
LEU
70
A
GLU
71
n
71
GLU
71
A
ALA
72
n
72
ALA
72
A
GLN
73
n
73
GLN
73
A
ASN
74
n
74
ASN
74
A
ARG
75
n
75
ARG
75
A
ILE
76
n
76
ILE
76
A
LYS
77
n
77
LYS
77
A
GLY
78
n
78
GLY
78
A
CYS
79
n
79
CYS
79
A
HIS
80
n
80
HIS
80
A
ASP
81
n
81
ASP
81
A
HIS
82
n
82
HIS
82
A
LEU
83
n
83
LEU
83
A
THR
84
n
84
THR
84
A
LEU
85
n
85
LEU
85
A
SER
86
n
86
SER
86
A
VAL
87
n
87
VAL
87
A
SER
88
n
88
SER
88
A
SER
89
n
89
SER
89
A
GLY
90
n
90
GLY
90
A
PRO
91
n
91
PRO
91
A
SER
92
n
92
SER
92
A
SER
93
n
93
SER
93
A
GLY
94
n
94
GLY
94
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
VAL
12
A
N
VAL
12
A
O
LEU
85
A
O
LEU
85
A
O
SER
86
A
O
SER
86
A
N
GLN
57
A
N
GLN
57
A
N
ILE
59
A
N
ILE
59
A
O
GLU
62
A
O
GLU
62
A
N
VAL
25
A
N
VAL
25
A
O
THR
35
A
O
THR
35
1
A
PRO
17
-69.74
-163.50
2
A
PRO
17
-69.76
-163.15
2
A
PRO
19
-69.75
-178.18
2
A
HIS
40
-54.28
173.90
2
A
ASP
81
-96.41
-68.25
3
A
PRO
17
-69.76
-166.86
3
A
PRO
19
-69.74
-178.81
4
A
PRO
17
-69.74
-163.47
4
A
HIS
80
-96.34
-68.17
4
A
ASP
81
-94.83
-66.79
5
A
PRO
17
-69.71
-163.51
5
A
PRO
19
-69.71
-178.37
5
A
HIS
80
-91.47
-61.67
5
A
ASP
81
-59.55
177.16
6
A
PRO
17
-69.81
-165.56
6
A
GLU
65
-56.22
-71.01
6
A
HIS
80
-96.98
-64.77
6
A
ASP
81
-91.94
-66.47
7
A
PRO
19
-69.78
-178.21
7
A
HIS
40
-52.11
170.66
7
A
PRO
91
-69.75
2.68
8
A
PRO
17
-69.76
-163.38
8
A
PRO
19
-69.74
-176.40
8
A
SER
43
-54.30
173.12
9
A
PRO
17
-69.70
-164.08
9
A
PRO
91
-69.76
-178.88
10
A
PRO
17
-69.82
-164.38
10
A
PRO
19
-69.78
-174.80
10
A
HIS
80
-97.46
-68.19
10
A
ASP
81
-97.70
-66.00
11
A
PRO
17
-69.78
-171.12
11
A
SER
43
-58.94
171.29
12
A
PRO
17
-69.74
-163.77
12
A
PRO
19
-69.78
-177.65
12
A
SER
43
-54.65
170.98
12
A
GLU
65
-62.67
-70.48
12
A
HIS
80
-97.45
-60.57
12
A
ASP
81
-98.01
-63.05
13
A
ASP
81
-58.38
178.09
14
A
PRO
17
-69.73
-168.26
14
A
PRO
19
-69.80
-178.17
15
A
PRO
17
-69.78
-164.50
15
A
PRO
19
-69.82
-178.25
15
A
ASN
74
-38.73
-38.35
15
A
PRO
91
-69.79
-172.45
16
A
PRO
17
-69.81
-168.69
16
A
PRO
19
-69.77
-173.14
16
A
HIS
40
-57.97
172.75
17
A
PRO
17
-69.74
-164.31
17
A
PRO
91
-69.81
90.19
18
A
PRO
17
-69.79
-164.62
18
A
PRO
19
-69.76
-176.91
19
A
PRO
17
-69.79
-167.59
19
A
PRO
19
-69.77
-173.76
20
A
PRO
17
-69.76
-163.52
20
A
PRO
19
-69.81
-177.19
20
A
GLU
65
-63.04
-70.23
Solution Structure of PDZ domain of PDZ and LIM domain protein
1
N
N
A
SER
43
A
SER
43
HELX_P
A
ALA
48
A
ALA
48
1
1
6
A
THR
68
A
THR
68
HELX_P
A
GLY
78
A
GLY
78
1
2
11
METAL BINDING PROTEIN
pdz domain, pdz and lim domain, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, METAL BINDING PROTEIN
A
GLY
16
A
GLY
16
1
A
PRO
17
A
PRO
17
0.05
A
SER
18
A
SER
18
1
A
PRO
19
A
PRO
19
-0.04
A
GLY
16
A
GLY
16
2
A
PRO
17
A
PRO
17
0.02
A
SER
18
A
SER
18
2
A
PRO
19
A
PRO
19
-0.07
A
GLY
16
A
GLY
16
3
A
PRO
17
A
PRO
17
0.00
A
SER
18
A
SER
18
3
A
PRO
19
A
PRO
19
-0.08
A
GLY
16
A
GLY
16
4
A
PRO
17
A
PRO
17
0.03
A
SER
18
A
SER
18
4
A
PRO
19
A
PRO
19
-0.14
A
GLY
16
A
GLY
16
5
A
PRO
17
A
PRO
17
0.01
A
SER
18
A
SER
18
5
A
PRO
19
A
PRO
19
-0.05
A
GLY
16
A
GLY
16
6
A
PRO
17
A
PRO
17
0.09
A
SER
18
A
SER
18
6
A
PRO
19
A
PRO
19
-0.03
A
GLY
16
A
GLY
16
7
A
PRO
17
A
PRO
17
0.05
A
SER
18
A
SER
18
7
A
PRO
19
A
PRO
19
0.04
A
GLY
16
A
GLY
16
8
A
PRO
17
A
PRO
17
0.01
A
SER
18
A
SER
18
8
A
PRO
19
A
PRO
19
-0.05
A
GLY
16
A
GLY
16
9
A
PRO
17
A
PRO
17
0.00
A
SER
18
A
SER
18
9
A
PRO
19
A
PRO
19
-0.07
A
GLY
16
A
GLY
16
10
A
PRO
17
A
PRO
17
0.10
A
SER
18
A
SER
18
10
A
PRO
19
A
PRO
19
0.04
A
GLY
16
A
GLY
16
11
A
PRO
17
A
PRO
17
0.07
A
SER
18
A
SER
18
11
A
PRO
19
A
PRO
19
0.03
A
GLY
16
A
GLY
16
12
A
PRO
17
A
PRO
17
0.04
A
SER
18
A
SER
18
12
A
PRO
19
A
PRO
19
0.00
A
GLY
16
A
GLY
16
13
A
PRO
17
A
PRO
17
0.02
A
SER
18
A
SER
18
13
A
PRO
19
A
PRO
19
-0.04
A
GLY
16
A
GLY
16
14
A
PRO
17
A
PRO
17
0.05
A
SER
18
A
SER
18
14
A
PRO
19
A
PRO
19
0.04
A
GLY
16
A
GLY
16
15
A
PRO
17
A
PRO
17
0.07
A
SER
18
A
SER
18
15
A
PRO
19
A
PRO
19
0.04
A
GLY
16
A
GLY
16
16
A
PRO
17
A
PRO
17
0.09
A
SER
18
A
SER
18
16
A
PRO
19
A
PRO
19
-0.06
A
GLY
16
A
GLY
16
17
A
PRO
17
A
PRO
17
0.04
A
SER
18
A
SER
18
17
A
PRO
19
A
PRO
19
-0.07
A
GLY
16
A
GLY
16
18
A
PRO
17
A
PRO
17
0.05
A
SER
18
A
SER
18
18
A
PRO
19
A
PRO
19
-0.01
A
GLY
16
A
GLY
16
19
A
PRO
17
A
PRO
17
0.07
A
SER
18
A
SER
18
19
A
PRO
19
A
PRO
19
0.00
A
GLY
16
A
GLY
16
20
A
PRO
17
A
PRO
17
0.05
A
SER
18
A
SER
18
20
A
PRO
19
A
PRO
19
0.01
PDLI4_HUMAN
UNP
1
1
P50479
MPHSVTLRGPSPWGFRLVGGRDFSAPLTISRVHAGSKAALAALCPGDLIQAINGESTELMTHLEAQNRIKGCHDHLTLSV
S
1
81
2EEG
8
88
P50479
A
1
8
88
1
expression tag
GLY
1
2EEG
A
P50479
UNP
1
1
expression tag
SER
2
2EEG
A
P50479
UNP
2
1
expression tag
SER
3
2EEG
A
P50479
UNP
3
1
expression tag
GLY
4
2EEG
A
P50479
UNP
4
1
expression tag
SER
5
2EEG
A
P50479
UNP
5
1
expression tag
SER
6
2EEG
A
P50479
UNP
6
1
expression tag
GLY
7
2EEG
A
P50479
UNP
7
1
expression tag
SER
89
2EEG
A
P50479
UNP
89
1
expression tag
GLY
90
2EEG
A
P50479
UNP
90
1
expression tag
PRO
91
2EEG
A
P50479
UNP
91
1
expression tag
SER
92
2EEG
A
P50479
UNP
92
1
expression tag
SER
93
2EEG
A
P50479
UNP
93
1
expression tag
GLY
94
2EEG
A
P50479
UNP
94
4
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
HIS
10
A
HIS
10
A
LEU
14
A
LEU
14
A
LEU
83
A
LEU
83
A
SER
88
A
SER
88
A
LEU
55
A
LEU
55
A
ILE
59
A
ILE
59
A
GLU
62
A
GLU
62
A
SER
63
A
SER
63
A
LEU
24
A
LEU
24
A
VAL
25
A
VAL
25
A
THR
35
A
THR
35
A
ILE
36
A
ILE
36