1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Nagashima, T.
Hayashi, F.
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
Solution structure of the first ig domain of human palladin
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
11923.438
palladin
IG
1
man
polymer
no
no
GSSGSSGAPFFEMKLKHYKIFEGMPVTFTCRVAGNPKPKIYWFKDGKQISPKSDHYTIQRDLDGTCSLHTTASTLDDDGN
YTIMAANPQGRISCTGRLMVQAVNSGPSSG
GSSGSSGAPFFEMKLKHYKIFEGMPVTFTCRVAGNPKPKIYWFKDGKQISPKSDHYTIQRDLDGTCSLHTTASTLDDDGN
YTIMAANPQGRISCTGRLMVQAVNSGPSSG
A
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
human
Homo
sample
Cell-free protein synthesis
KIAA0992
9606
Homo sapiens
plasmid
P050711-06
RIKEN Structural Genomics/Proteomics Initiative
RSGI
NPPSFA, National Project on Protein Structural and Functional Analyses
repository
Initial release
Version format compliance
Version format compliance
1
0
2007-04-24
1
1
2008-04-30
1
2
2011-07-13
Y
PDBJ
Y
PDBJ
2006-04-20
REL
REL
target function, structures with the lowest energy
100
20
3D_15N-separated_NOESY
3D_13C-separated_NOESY
120mM
7.0
ambient
293
K
torsion angle dynamics
1
lowest energy
0.76mM uniformly 13C and 15N labeled protein; 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3, 10% D2O, 90% H2O
10% D2O, 90% H2O
Varian
collection
VNMR
6.1C
Delaglio, F.
processing
NMRPipe
20020425
Johnson, B.A.
data analysis
NMRView
5.0.4
Kobayashi, N.
data analysis
Kujira
0.9318
Guntert, P.
structure solution
CYANA
2.0.17
Guntert, P.
refinement
CYANA
2.0.17
800
Varian
INOVA
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
ALA
8
n
8
ALA
8
A
PRO
9
n
9
PRO
9
A
PHE
10
n
10
PHE
10
A
PHE
11
n
11
PHE
11
A
GLU
12
n
12
GLU
12
A
MET
13
n
13
MET
13
A
LYS
14
n
14
LYS
14
A
LEU
15
n
15
LEU
15
A
LYS
16
n
16
LYS
16
A
HIS
17
n
17
HIS
17
A
TYR
18
n
18
TYR
18
A
LYS
19
n
19
LYS
19
A
ILE
20
n
20
ILE
20
A
PHE
21
n
21
PHE
21
A
GLU
22
n
22
GLU
22
A
GLY
23
n
23
GLY
23
A
MET
24
n
24
MET
24
A
PRO
25
n
25
PRO
25
A
VAL
26
n
26
VAL
26
A
THR
27
n
27
THR
27
A
PHE
28
n
28
PHE
28
A
THR
29
n
29
THR
29
A
CYS
30
n
30
CYS
30
A
ARG
31
n
31
ARG
31
A
VAL
32
n
32
VAL
32
A
ALA
33
n
33
ALA
33
A
GLY
34
n
34
GLY
34
A
ASN
35
n
35
ASN
35
A
PRO
36
n
36
PRO
36
A
LYS
37
n
37
LYS
37
A
PRO
38
n
38
PRO
38
A
LYS
39
n
39
LYS
39
A
ILE
40
n
40
ILE
40
A
TYR
41
n
41
TYR
41
A
TRP
42
n
42
TRP
42
A
PHE
43
n
43
PHE
43
A
LYS
44
n
44
LYS
44
A
ASP
45
n
45
ASP
45
A
GLY
46
n
46
GLY
46
A
LYS
47
n
47
LYS
47
A
GLN
48
n
48
GLN
48
A
ILE
49
n
49
ILE
49
A
SER
50
n
50
SER
50
A
PRO
51
n
51
PRO
51
A
LYS
52
n
52
LYS
52
A
SER
53
n
53
SER
53
A
ASP
54
n
54
ASP
54
A
HIS
55
n
55
HIS
55
A
TYR
56
n
56
TYR
56
A
THR
57
n
57
THR
57
A
ILE
58
n
58
ILE
58
A
GLN
59
n
59
GLN
59
A
ARG
60
n
60
ARG
60
A
ASP
61
n
61
ASP
61
A
LEU
62
n
62
LEU
62
A
ASP
63
n
63
ASP
63
A
GLY
64
n
64
GLY
64
A
THR
65
n
65
THR
65
A
CYS
66
n
66
CYS
66
A
SER
67
n
67
SER
67
A
LEU
68
n
68
LEU
68
A
HIS
69
n
69
HIS
69
A
THR
70
n
70
THR
70
A
THR
71
n
71
THR
71
A
ALA
72
n
72
ALA
72
A
SER
73
n
73
SER
73
A
THR
74
n
74
THR
74
A
LEU
75
n
75
LEU
75
A
ASP
76
n
76
ASP
76
A
ASP
77
n
77
ASP
77
A
ASP
78
n
78
ASP
78
A
GLY
79
n
79
GLY
79
A
ASN
80
n
80
ASN
80
A
TYR
81
n
81
TYR
81
A
THR
82
n
82
THR
82
A
ILE
83
n
83
ILE
83
A
MET
84
n
84
MET
84
A
ALA
85
n
85
ALA
85
A
ALA
86
n
86
ALA
86
A
ASN
87
n
87
ASN
87
A
PRO
88
n
88
PRO
88
A
GLN
89
n
89
GLN
89
A
GLY
90
n
90
GLY
90
A
ARG
91
n
91
ARG
91
A
ILE
92
n
92
ILE
92
A
SER
93
n
93
SER
93
A
CYS
94
n
94
CYS
94
A
THR
95
n
95
THR
95
A
GLY
96
n
96
GLY
96
A
ARG
97
n
97
ARG
97
A
LEU
98
n
98
LEU
98
A
MET
99
n
99
MET
99
A
VAL
100
n
100
VAL
100
A
GLN
101
n
101
GLN
101
A
ALA
102
n
102
ALA
102
A
VAL
103
n
103
VAL
103
A
ASN
104
n
104
ASN
104
A
SER
105
n
105
SER
105
A
GLY
106
n
106
GLY
106
A
PRO
107
n
107
PRO
107
A
SER
108
n
108
SER
108
A
SER
109
n
109
SER
109
A
GLY
110
n
110
GLY
110
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
ILE
20
A
N
ILE
20
A
O
MET
99
A
O
MET
99
A
N
PHE
28
A
N
PHE
28
A
O
LEU
68
A
O
LEU
68
A
O
HIS
69
A
O
HIS
69
A
N
THR
57
A
N
THR
57
A
N
PHE
43
A
N
PHE
43
A
O
THR
82
A
O
THR
82
A
N
ILE
83
A
N
ILE
83
A
O
CYS
94
A
O
CYS
94
1
A
LYS
37
-34.96
97.90
1
A
ASP
45
34.62
48.85
1
A
LYS
52
-92.11
34.97
1
A
ASP
78
-47.55
163.04
1
A
PRO
88
-69.76
4.57
1
A
SER
109
-48.55
96.30
2
A
LYS
14
-46.22
154.14
2
A
LYS
37
-32.21
99.44
2
A
ASP
63
-98.99
32.21
2
A
PRO
88
-69.72
4.33
2
A
SER
109
-174.92
112.12
3
A
SER
2
-93.33
41.91
3
A
MET
13
-119.78
69.98
3
A
LYS
14
-39.56
134.51
3
A
GLU
22
-39.52
125.77
3
A
LYS
37
-35.13
106.52
3
A
ASP
45
39.87
30.07
3
A
LYS
52
-83.29
35.00
3
A
PRO
88
-69.75
4.09
4
A
LYS
14
-47.85
156.93
4
A
SER
53
-36.20
142.09
4
A
ASP
78
-39.73
158.58
4
A
PRO
88
-69.73
4.92
5
A
LYS
37
-40.15
107.48
5
A
ASP
45
35.42
35.06
5
A
PRO
88
-69.79
2.44
6
A
LYS
37
-35.38
99.64
6
A
SER
53
-57.94
97.33
6
A
ASP
54
-36.48
-38.45
6
A
ASP
78
-44.77
160.87
6
A
PRO
88
-69.76
4.42
6
A
SER
105
-170.53
139.23
7
A
SER
3
-95.22
57.46
7
A
PRO
36
-69.79
-171.06
7
A
LYS
37
-53.53
108.01
7
A
ASP
45
37.09
29.33
7
A
LYS
52
-84.30
34.06
7
A
ASP
54
-34.52
-33.02
7
A
PRO
88
-69.72
4.54
7
A
SER
109
37.30
42.48
8
A
SER
2
-174.04
112.17
8
A
PRO
36
-69.81
-177.51
8
A
LYS
37
-46.11
109.65
8
A
ASP
45
37.37
28.63
8
A
LYS
52
-97.08
37.72
8
A
SER
53
-55.30
-174.32
8
A
PRO
88
-69.75
3.56
9
A
LYS
14
-46.37
164.40
9
A
LYS
37
-32.31
111.53
9
A
LYS
52
-90.08
39.55
9
A
PRO
88
-69.85
5.41
9
A
ASN
104
-107.94
75.03
9
A
SER
108
-126.73
-50.00
10
A
LYS
14
-44.00
152.86
10
A
LEU
15
-56.47
101.71
10
A
LYS
37
-39.71
122.61
10
A
ASP
45
41.07
27.77
10
A
SER
53
-38.80
94.63
10
A
PRO
88
-69.76
4.95
10
A
ALA
102
-55.62
107.71
10
A
PRO
107
-69.74
1.47
11
A
LYS
14
-43.08
164.03
11
A
PRO
36
-69.76
-175.53
11
A
ASP
45
38.07
31.10
11
A
LYS
52
-90.80
31.34
11
A
ASP
78
-45.62
155.87
11
A
PRO
88
-69.80
4.86
12
A
LYS
14
-45.70
156.77
12
A
PRO
36
-69.74
-176.18
12
A
LYS
37
-53.90
109.67
12
A
SER
53
-36.37
128.00
12
A
PRO
88
-69.67
4.34
13
A
LYS
14
-49.79
154.76
13
A
LYS
37
-42.91
103.29
13
A
SER
53
-67.21
96.86
13
A
PRO
88
-69.76
6.17
14
A
LYS
14
-48.99
170.65
14
A
HIS
55
-44.43
-70.06
14
A
ASP
63
-84.27
33.89
14
A
LEU
75
-35.39
-37.45
14
A
ASP
77
-37.46
-28.86
14
A
PRO
88
-69.76
4.02
15
A
SER
2
-58.12
93.23
15
A
LYS
37
-34.07
136.64
15
A
ASP
45
43.34
28.84
15
A
HIS
55
-101.72
-71.78
15
A
LEU
75
-34.28
-38.43
15
A
PRO
88
-69.75
4.87
15
A
SER
109
-127.43
-60.46
16
A
ASP
45
34.55
49.11
16
A
LYS
52
-86.84
39.48
16
A
LEU
75
-37.30
-35.34
16
A
ASP
78
-38.37
149.66
16
A
PRO
88
-69.77
4.54
16
A
SER
105
-171.59
116.31
17
A
GLU
22
-35.38
128.41
17
A
PRO
36
-69.78
-174.61
17
A
ASP
78
-46.40
165.69
17
A
PRO
88
-69.79
5.08
17
A
PRO
107
-69.80
1.74
18
A
SER
3
-90.53
44.78
18
A
LYS
14
-48.46
161.06
18
A
ASP
45
47.04
25.71
18
A
PRO
88
-69.83
4.20
19
A
ASP
45
37.95
40.98
19
A
LYS
52
-89.85
33.78
19
A
PRO
88
-69.76
4.75
19
A
VAL
103
-114.96
51.76
19
A
SER
105
-131.41
-41.05
20
A
LEU
15
-34.93
119.37
20
A
LEU
75
-39.07
-37.49
20
A
PRO
88
-69.80
4.70
palladin
Solution structure of the first ig domain of human palladin
1
N
N
PROTEIN BINDING
beta-sandwich, KIAA0992, myopalladin, actin-associated scaffold, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, PROTEIN BINDING
A
ASN
35
A
ASN
35
1
A
PRO
36
A
PRO
36
-0.03
A
ASN
35
A
ASN
35
2
A
PRO
36
A
PRO
36
-0.07
A
ASN
35
A
ASN
35
3
A
PRO
36
A
PRO
36
-0.08
A
ASN
35
A
ASN
35
4
A
PRO
36
A
PRO
36
0.00
A
ASN
35
A
ASN
35
5
A
PRO
36
A
PRO
36
-0.04
A
ASN
35
A
ASN
35
6
A
PRO
36
A
PRO
36
-0.06
A
ASN
35
A
ASN
35
7
A
PRO
36
A
PRO
36
-0.07
A
ASN
35
A
ASN
35
8
A
PRO
36
A
PRO
36
-0.01
A
ASN
35
A
ASN
35
9
A
PRO
36
A
PRO
36
-0.02
A
ASN
35
A
ASN
35
10
A
PRO
36
A
PRO
36
-0.06
A
ASN
35
A
ASN
35
11
A
PRO
36
A
PRO
36
-0.04
A
ASN
35
A
ASN
35
12
A
PRO
36
A
PRO
36
-0.10
A
ASN
35
A
ASN
35
13
A
PRO
36
A
PRO
36
-0.02
A
ASN
35
A
ASN
35
14
A
PRO
36
A
PRO
36
-0.06
A
ASN
35
A
ASN
35
15
A
PRO
36
A
PRO
36
-0.02
A
ASN
35
A
ASN
35
16
A
PRO
36
A
PRO
36
-0.07
A
ASN
35
A
ASN
35
17
A
PRO
36
A
PRO
36
-0.03
A
ASN
35
A
ASN
35
18
A
PRO
36
A
PRO
36
-0.03
A
ASN
35
A
ASN
35
19
A
PRO
36
A
PRO
36
-0.04
A
ASN
35
A
ASN
35
20
A
PRO
36
A
PRO
36
-0.04
NP_057165
GB
1
776
21361585
APFFEMKLKHYKIFEGMPVTFTCRVAGNPKPKIYWFKDGKQISPKSDHYTIQRDLDGTCSLHTTASTLDDDGNYTIMAAN
PQGRISCTGRLMVQAVN
776
872
2DM2
8
104
21361585
A
1
8
104
1
CLONING ARTIFACT
GLY
1
2DM2
A
21361585
GB
1
1
CLONING ARTIFACT
SER
2
2DM2
A
21361585
GB
2
1
CLONING ARTIFACT
SER
3
2DM2
A
21361585
GB
3
1
CLONING ARTIFACT
GLY
4
2DM2
A
21361585
GB
4
1
CLONING ARTIFACT
SER
5
2DM2
A
21361585
GB
5
1
CLONING ARTIFACT
SER
6
2DM2
A
21361585
GB
6
1
CLONING ARTIFACT
GLY
7
2DM2
A
21361585
GB
7
1
CLONING ARTIFACT
SER
105
2DM2
A
21361585
GB
105
1
CLONING ARTIFACT
GLY
106
2DM2
A
21361585
GB
106
1
CLONING ARTIFACT
PRO
107
2DM2
A
21361585
GB
107
1
CLONING ARTIFACT
SER
108
2DM2
A
21361585
GB
108
1
CLONING ARTIFACT
SER
109
2DM2
A
21361585
GB
109
1
CLONING ARTIFACT
GLY
110
2DM2
A
21361585
GB
110
2
3
3
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TYR
18
A
TYR
18
A
PHE
21
A
PHE
21
A
LEU
98
A
LEU
98
A
GLN
101
A
GLN
101
A
VAL
26
A
VAL
26
A
ARG
31
A
ARG
31
A
THR
65
A
THR
65
A
THR
70
A
THR
70
A
TYR
56
A
TYR
56
A
ARG
60
A
ARG
60
A
LYS
39
A
LYS
39
A
PHE
43
A
PHE
43
A
THR
82
A
THR
82
A
ALA
86
A
ALA
86
A
ILE
92
A
ILE
92
A
CYS
94
A
CYS
94