1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Inoue, K.
Kurosaki, C.
Yoshida, M.
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 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 fifth SH3 domain from human KIAA0418 protein
10.2210/pdb2egc/pdb
pdb_00002egc
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
8155.835
SH3 and PX domain-containing protein 2A
SH3 domain
1
man
polymer
SH3 multiple domains protein 1, Five SH3 domain-containing protein, Adaptor protein TKS5, KIAA0418 protein
no
no
GSSGSSGNLKDVYVSIADYEGDEETAGFQEGVSMEVLERNPNGWWYCQILDGVKPFKGWVPSNYLEKKNSGPSSG
GSSGSSGNLKDVYVSIADYEGDEETAGFQEGVSMEVLERNPNGWWYCQILDGVKPFKGWVPSNYLEKKNSGPSSG
A
hsk002100407.4
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
human
Homo
sample
Cell-free protein synthesis
SH3PXD2A, FISH, KIAA0418, SH3MD1
9606
Homo sapiens
PLASMID
P050919-09
RIKEN Structural Genomics/Proteomics Initiative
RSGI
NPPSFA, National Project on Protein Structural and Functional Analyses
database_2
pdbx_nmr_software
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
2007-08-28
1
1
2011-07-13
1
2
2022-03-09
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_ref_seq_dif.details
SHEET
DETERMINATION METHOD: AUTHOR DETERMINED
Y
PDBJ
Y
PDBJ
2007-02-28
REL
structures with the least restraint violations,structures with the lowest energy,target function
100
20
3D_15N-separated_NOESY
3D_13C-separated_NOESY
120mM
7.0
ambient
298
K
torsion angle dynamics
1
lowest energy
1.18mM U-15N,13C-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
90% H2O/10% D2O
JEOL
collection
Delta NMR
4.3.2
Delaglio, F.
processing
NMRPipe
20060324
Johnson, B.A.
data analysis
NMRView
5.0.4
Kobayashi, N.
data analysis
KUJIRA
0.9807
Guntert, P.
structure solution
CYANA
2.1
Guntert, P.
refinement
CYANA
2.1
800
JEOL
ECA
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
ASN
8
n
8
ASN
8
A
LEU
9
n
9
LEU
9
A
LYS
10
n
10
LYS
10
A
ASP
11
n
11
ASP
11
A
VAL
12
n
12
VAL
12
A
TYR
13
n
13
TYR
13
A
VAL
14
n
14
VAL
14
A
SER
15
n
15
SER
15
A
ILE
16
n
16
ILE
16
A
ALA
17
n
17
ALA
17
A
ASP
18
n
18
ASP
18
A
TYR
19
n
19
TYR
19
A
GLU
20
n
20
GLU
20
A
GLY
21
n
21
GLY
21
A
ASP
22
n
22
ASP
22
A
GLU
23
n
23
GLU
23
A
GLU
24
n
24
GLU
24
A
THR
25
n
25
THR
25
A
ALA
26
n
26
ALA
26
A
GLY
27
n
27
GLY
27
A
PHE
28
n
28
PHE
28
A
GLN
29
n
29
GLN
29
A
GLU
30
n
30
GLU
30
A
GLY
31
n
31
GLY
31
A
VAL
32
n
32
VAL
32
A
SER
33
n
33
SER
33
A
MET
34
n
34
MET
34
A
GLU
35
n
35
GLU
35
A
VAL
36
n
36
VAL
36
A
LEU
37
n
37
LEU
37
A
GLU
38
n
38
GLU
38
A
ARG
39
n
39
ARG
39
A
ASN
40
n
40
ASN
40
A
PRO
41
n
41
PRO
41
A
ASN
42
n
42
ASN
42
A
GLY
43
n
43
GLY
43
A
TRP
44
n
44
TRP
44
A
TRP
45
n
45
TRP
45
A
TYR
46
n
46
TYR
46
A
CYS
47
n
47
CYS
47
A
GLN
48
n
48
GLN
48
A
ILE
49
n
49
ILE
49
A
LEU
50
n
50
LEU
50
A
ASP
51
n
51
ASP
51
A
GLY
52
n
52
GLY
52
A
VAL
53
n
53
VAL
53
A
LYS
54
n
54
LYS
54
A
PRO
55
n
55
PRO
55
A
PHE
56
n
56
PHE
56
A
LYS
57
n
57
LYS
57
A
GLY
58
n
58
GLY
58
A
TRP
59
n
59
TRP
59
A
VAL
60
n
60
VAL
60
A
PRO
61
n
61
PRO
61
A
SER
62
n
62
SER
62
A
ASN
63
n
63
ASN
63
A
TYR
64
n
64
TYR
64
A
LEU
65
n
65
LEU
65
A
GLU
66
n
66
GLU
66
A
LYS
67
n
67
LYS
67
A
LYS
68
n
68
LYS
68
A
ASN
69
n
69
ASN
69
A
SER
70
n
70
SER
70
A
GLY
71
n
71
GLY
71
A
PRO
72
n
72
PRO
72
A
SER
73
n
73
SER
73
A
SER
74
n
74
SER
74
A
GLY
75
n
75
GLY
75
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
36
A
N
VAL
36
A
O
ASP
11
A
O
ASP
11
A
N
VAL
14
A
N
VAL
14
A
O
GLU
66
A
O
GLU
66
A
N
GLU
38
A
N
GLU
38
A
O
TYR
46
A
O
TYR
46
A
N
TRP
45
A
N
TRP
45
A
O
VAL
60
A
O
VAL
60
1
A
SER
3
-87.58
-72.88
1
A
ALA
17
-177.55
143.37
1
A
ASP
22
-66.19
-176.47
1
A
LEU
50
-98.67
42.93
1
A
LYS
54
-164.26
69.92
2
A
SER
5
-122.26
-58.67
2
A
ALA
17
-178.06
146.40
2
A
LEU
50
-98.37
42.91
2
A
LYS
54
-155.22
70.16
3
A
LYS
10
-174.85
107.86
3
A
ALA
17
-177.98
137.43
3
A
LEU
50
-104.99
41.06
3
A
LYS
54
-164.40
73.68
3
A
ASN
69
-55.79
104.25
3
A
PRO
72
-69.71
84.97
4
A
ASP
11
-100.81
54.40
4
A
ALA
17
-178.16
147.97
4
A
LEU
50
-98.31
42.99
4
A
LYS
54
-152.49
68.30
4
A
TYR
64
-95.82
33.74
4
A
PRO
72
-69.76
-176.35
5
A
ASN
8
-124.98
-71.94
5
A
ALA
17
-177.23
142.77
5
A
LEU
50
-100.00
42.93
5
A
LYS
54
-170.32
68.28
5
A
TYR
64
-95.79
33.88
6
A
SER
2
-128.09
-61.70
6
A
ALA
17
-177.44
148.90
6
A
LEU
50
-99.30
43.01
6
A
LYS
54
-161.64
71.56
6
A
TYR
64
-95.85
33.93
7
A
ASP
11
-91.47
56.39
7
A
ALA
17
-176.84
148.77
7
A
ASP
22
-65.85
-176.35
7
A
LEU
50
-99.36
43.21
7
A
LYS
54
-166.66
72.23
7
A
TYR
64
-95.78
33.76
7
A
SER
70
-110.53
68.92
7
A
PRO
72
-69.75
-178.73
8
A
ASP
11
-98.15
51.26
8
A
ALA
17
-177.25
147.57
8
A
LEU
50
-99.67
43.07
8
A
LYS
54
-167.15
72.32
8
A
TYR
64
-95.77
33.71
9
A
SER
5
-130.75
-69.46
9
A
ALA
17
-176.77
149.83
9
A
ASP
22
-59.86
178.94
9
A
LEU
50
-98.58
42.61
9
A
LYS
54
-167.36
68.31
9
A
TYR
64
-95.82
34.23
10
A
SER
2
-94.36
-68.68
10
A
ASP
22
-58.90
178.07
10
A
LEU
50
-100.04
42.47
10
A
LYS
54
-166.61
72.37
10
A
TYR
64
-95.77
34.01
10
A
LYS
67
-59.44
108.09
11
A
ALA
17
-177.20
147.75
11
A
ASP
22
-63.84
-177.06
11
A
LEU
50
-99.06
43.27
11
A
LYS
54
-167.35
72.10
11
A
TYR
64
-95.78
33.76
11
A
LYS
67
-56.80
108.23
11
A
SER
74
-95.93
48.47
12
A
ALA
17
-177.04
149.99
12
A
LEU
50
-99.19
42.95
12
A
LYS
54
-167.13
72.43
12
A
TYR
64
-95.75
33.80
13
A
LEU
9
-58.62
177.18
13
A
LYS
10
63.50
105.94
13
A
LEU
50
-101.14
42.79
13
A
LYS
54
-160.53
72.31
14
A
ASP
11
-117.27
60.26
14
A
ALA
17
-177.03
147.46
14
A
ASP
22
-126.95
-74.92
14
A
GLU
23
-136.04
-49.14
14
A
LEU
50
-98.72
42.93
14
A
LYS
54
-165.20
69.42
14
A
PRO
72
-69.68
-171.13
14
A
SER
73
-129.50
-56.07
15
A
ALA
17
-176.64
146.02
15
A
ASP
22
-62.28
-177.48
15
A
LEU
50
-100.42
42.82
15
A
LYS
54
-159.23
68.27
15
A
TYR
64
-96.07
30.78
16
A
SER
6
-55.88
175.84
16
A
LEU
9
52.97
86.09
16
A
LEU
50
-101.42
42.16
16
A
LYS
54
-161.62
72.53
16
A
TYR
64
-95.78
33.81
17
A
LEU
50
-98.77
43.14
17
A
TYR
64
-95.72
33.73
18
A
ALA
17
-177.45
145.32
18
A
ASP
22
-122.30
-74.96
18
A
GLU
23
-132.91
-74.46
18
A
LEU
50
-103.25
42.18
18
A
LYS
54
-171.35
68.31
18
A
TYR
64
-95.91
32.50
19
A
ASP
11
-108.71
52.71
19
A
ASP
22
-66.49
-179.58
19
A
LEU
50
-98.88
41.96
19
A
LYS
54
-152.62
68.27
19
A
TYR
64
-95.80
33.86
20
A
ASP
22
-61.13
-174.84
20
A
LEU
50
-102.95
41.47
20
A
LYS
54
-161.50
68.51
20
A
TYR
64
-95.70
34.20
Solution structure of the fifth SH3 domain from human KIAA0418 protein
1
N
N
SIGNALING PROTEIN
SH3 domain, KIAA0418 protein, SH3MD1, SH3 multiple domains 1, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, SIGNALING PROTEIN
SPD2A_HUMAN
UNP
1
1072
Q5TCZ1
NLKDVYVSIADYEGDEETAGFQEGVSMEVLERNPNGWWYCQILDGVKPFKGWVPSNYLEKKN
1072
1133
2EGC
8
69
Q5TCZ1
A
1
8
69
1
expression tag
GLY
1
2EGC
A
Q5TCZ1
UNP
1
1
expression tag
SER
2
2EGC
A
Q5TCZ1
UNP
2
1
expression tag
SER
3
2EGC
A
Q5TCZ1
UNP
3
1
expression tag
GLY
4
2EGC
A
Q5TCZ1
UNP
4
1
expression tag
SER
5
2EGC
A
Q5TCZ1
UNP
5
1
expression tag
SER
6
2EGC
A
Q5TCZ1
UNP
6
1
expression tag
GLY
7
2EGC
A
Q5TCZ1
UNP
7
1
expression tag
SER
70
2EGC
A
Q5TCZ1
UNP
70
1
expression tag
GLY
71
2EGC
A
Q5TCZ1
UNP
71
1
expression tag
PRO
72
2EGC
A
Q5TCZ1
UNP
72
1
expression tag
SER
73
2EGC
A
Q5TCZ1
UNP
73
1
expression tag
SER
74
2EGC
A
Q5TCZ1
UNP
74
1
expression tag
GLY
75
2EGC
A
Q5TCZ1
UNP
75
3
3
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
SER
33
A
SER
33
A
VAL
36
A
VAL
36
A
ASP
11
A
ASP
11
A
SER
15
A
SER
15
A
LEU
65
A
LEU
65
A
LYS
67
A
LYS
67
A
GLU
38
A
GLU
38
A
ARG
39
A
ARG
39
A
TRP
44
A
TRP
44
A
ILE
49
A
ILE
49
A
PHE
56
A
PHE
56
A
PRO
61
A
PRO
61