1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Li, H.
Tomizawa, T.
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
Solution structure of the PH domain of Pleckstrin homology domain-containing protein family B member 1 from mouse
10.2210/pdb2d9v/pdb
pdb_00002d9v
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
14395.934
Pleckstrin homology domain-containing protein family B member 1
PH domain
1
man
polymer
Pleckstrin homology domain retinal protein 1, PH domain containing protein in retina 1, PHRET1
no
no
GSSGSSGLVRGGWLWRQSSILRRWKRNWFALWLDGTLGYYHDETAQDEEDRVVIHFNVRDIKVGQECQDVQPPEGRSRDG
LLTVNLREGSRLHLCAETRDDAIAWKTALMEANSTPAPAGATVPSGPSSG
GSSGSSGLVRGGWLWRQSSILRRWKRNWFALWLDGTLGYYHDETAQDEEDRVVIHFNVRDIKVGQECQDVQPPEGRSRDG
LLTVNLREGSRLHLCAETRDDAIAWKTALMEANSTPAPAGATVPSGPSSG
A
mmi002018667.1
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
n
n
n
n
n
n
n
n
n
house mouse
Mus
sample
Cell-free protein synthesis
Phr1
10090
Mus musculus
PLASMID
P050302-02
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
2006-06-13
1
1
2008-04-30
1
2
2011-07-13
1
3
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
HELIX
Determination Method: Author determined
SHEET
Determination Method: Author determined
Y
PDBJ
Y
PDBJ
2005-12-13
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
1.12mM PH domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O,10% D2O
90% H2O/10% D2O
Bruker
collection
XwinNMR
3.5
Delaglio, F.
processing
NMRPipe
20030801
Johnson, B.A.
data analysis
NMRView
5.0.4
Kobayashi, N.
data analysis
KUJIRA
0.932
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
LEU
8
n
8
LEU
8
A
VAL
9
n
9
VAL
9
A
ARG
10
n
10
ARG
10
A
GLY
11
n
11
GLY
11
A
GLY
12
n
12
GLY
12
A
TRP
13
n
13
TRP
13
A
LEU
14
n
14
LEU
14
A
TRP
15
n
15
TRP
15
A
ARG
16
n
16
ARG
16
A
GLN
17
n
17
GLN
17
A
SER
18
n
18
SER
18
A
SER
19
n
19
SER
19
A
ILE
20
n
20
ILE
20
A
LEU
21
n
21
LEU
21
A
ARG
22
n
22
ARG
22
A
ARG
23
n
23
ARG
23
A
TRP
24
n
24
TRP
24
A
LYS
25
n
25
LYS
25
A
ARG
26
n
26
ARG
26
A
ASN
27
n
27
ASN
27
A
TRP
28
n
28
TRP
28
A
PHE
29
n
29
PHE
29
A
ALA
30
n
30
ALA
30
A
LEU
31
n
31
LEU
31
A
TRP
32
n
32
TRP
32
A
LEU
33
n
33
LEU
33
A
ASP
34
n
34
ASP
34
A
GLY
35
n
35
GLY
35
A
THR
36
n
36
THR
36
A
LEU
37
n
37
LEU
37
A
GLY
38
n
38
GLY
38
A
TYR
39
n
39
TYR
39
A
TYR
40
n
40
TYR
40
A
HIS
41
n
41
HIS
41
A
ASP
42
n
42
ASP
42
A
GLU
43
n
43
GLU
43
A
THR
44
n
44
THR
44
A
ALA
45
n
45
ALA
45
A
GLN
46
n
46
GLN
46
A
ASP
47
n
47
ASP
47
A
GLU
48
n
48
GLU
48
A
GLU
49
n
49
GLU
49
A
ASP
50
n
50
ASP
50
A
ARG
51
n
51
ARG
51
A
VAL
52
n
52
VAL
52
A
VAL
53
n
53
VAL
53
A
ILE
54
n
54
ILE
54
A
HIS
55
n
55
HIS
55
A
PHE
56
n
56
PHE
56
A
ASN
57
n
57
ASN
57
A
VAL
58
n
58
VAL
58
A
ARG
59
n
59
ARG
59
A
ASP
60
n
60
ASP
60
A
ILE
61
n
61
ILE
61
A
LYS
62
n
62
LYS
62
A
VAL
63
n
63
VAL
63
A
GLY
64
n
64
GLY
64
A
GLN
65
n
65
GLN
65
A
GLU
66
n
66
GLU
66
A
CYS
67
n
67
CYS
67
A
GLN
68
n
68
GLN
68
A
ASP
69
n
69
ASP
69
A
VAL
70
n
70
VAL
70
A
GLN
71
n
71
GLN
71
A
PRO
72
n
72
PRO
72
A
PRO
73
n
73
PRO
73
A
GLU
74
n
74
GLU
74
A
GLY
75
n
75
GLY
75
A
ARG
76
n
76
ARG
76
A
SER
77
n
77
SER
77
A
ARG
78
n
78
ARG
78
A
ASP
79
n
79
ASP
79
A
GLY
80
n
80
GLY
80
A
LEU
81
n
81
LEU
81
A
LEU
82
n
82
LEU
82
A
THR
83
n
83
THR
83
A
VAL
84
n
84
VAL
84
A
ASN
85
n
85
ASN
85
A
LEU
86
n
86
LEU
86
A
ARG
87
n
87
ARG
87
A
GLU
88
n
88
GLU
88
A
GLY
89
n
89
GLY
89
A
SER
90
n
90
SER
90
A
ARG
91
n
91
ARG
91
A
LEU
92
n
92
LEU
92
A
HIS
93
n
93
HIS
93
A
LEU
94
n
94
LEU
94
A
CYS
95
n
95
CYS
95
A
ALA
96
n
96
ALA
96
A
GLU
97
n
97
GLU
97
A
THR
98
n
98
THR
98
A
ARG
99
n
99
ARG
99
A
ASP
100
n
100
ASP
100
A
ASP
101
n
101
ASP
101
A
ALA
102
n
102
ALA
102
A
ILE
103
n
103
ILE
103
A
ALA
104
n
104
ALA
104
A
TRP
105
n
105
TRP
105
A
LYS
106
n
106
LYS
106
A
THR
107
n
107
THR
107
A
ALA
108
n
108
ALA
108
A
LEU
109
n
109
LEU
109
A
MET
110
n
110
MET
110
A
GLU
111
n
111
GLU
111
A
ALA
112
n
112
ALA
112
A
ASN
113
n
113
ASN
113
A
SER
114
n
114
SER
114
A
THR
115
n
115
THR
115
A
PRO
116
n
116
PRO
116
A
ALA
117
n
117
ALA
117
A
PRO
118
n
118
PRO
118
A
ALA
119
n
119
ALA
119
A
GLY
120
n
120
GLY
120
A
ALA
121
n
121
ALA
121
A
THR
122
n
122
THR
122
A
VAL
123
n
123
VAL
123
A
PRO
124
n
124
PRO
124
A
SER
125
n
125
SER
125
A
GLY
126
n
126
GLY
126
A
PRO
127
n
127
PRO
127
A
SER
128
n
128
SER
128
A
SER
129
n
129
SER
129
A
GLY
130
n
130
GLY
130
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
O
VAL
52
A
O
VAL
52
A
N
LEU
37
A
N
LEU
37
A
O
THR
36
A
O
THR
36
A
N
TRP
32
A
N
TRP
32
A
O
ASN
27
A
O
ASN
27
A
N
LEU
14
A
N
LEU
14
A
N
TRP
15
A
N
TRP
15
A
O
CYS
95
A
O
CYS
95
A
O
LEU
92
A
O
LEU
92
A
N
VAL
84
A
N
VAL
84
A
O
ASN
85
A
O
ASN
85
A
N
ASP
60
A
N
ASP
60
1
A
ASP
47
-117.93
79.13
1
A
PHE
56
37.05
47.40
1
A
CYS
67
-41.53
151.07
1
A
GLN
68
-130.93
-41.47
1
A
PRO
73
-69.78
-165.77
1
A
ARG
76
-48.09
176.98
1
A
LEU
81
-36.74
151.93
1
A
PRO
118
-69.76
2.81
1
A
ALA
119
-34.14
110.85
1
A
PRO
124
-69.76
2.75
1
A
SER
125
-34.61
131.84
1
A
SER
128
-129.69
-55.05
2
A
ARG
22
34.58
37.70
2
A
ALA
45
-82.14
40.36
2
A
ASP
47
-90.59
42.16
2
A
GLU
48
-37.55
114.76
2
A
PHE
56
36.82
42.74
2
A
GLN
68
-120.19
-63.25
2
A
PRO
73
-69.78
-172.94
2
A
LEU
81
-37.82
142.51
2
A
PRO
118
-69.71
2.78
2
A
SER
128
-90.53
48.44
3
A
SER
3
-122.79
-54.31
3
A
SER
6
-170.77
106.39
3
A
ARG
22
34.44
41.04
3
A
THR
44
-67.16
98.81
3
A
ALA
45
-82.40
44.67
3
A
ASP
47
-87.85
43.72
3
A
GLU
48
-35.81
102.83
3
A
PHE
56
38.32
47.03
3
A
GLU
66
-34.76
-33.74
3
A
CYS
67
-45.41
167.11
3
A
GLN
68
-132.66
-53.78
3
A
GLU
74
-37.57
120.61
3
A
ARG
76
-52.72
173.56
3
A
SER
90
-174.64
139.22
3
A
THR
115
-165.71
105.04
3
A
PRO
116
-69.85
-177.98
4
A
SER
6
-54.06
-176.93
4
A
VAL
9
-91.29
-61.64
4
A
GLU
43
-39.88
-27.12
4
A
THR
44
-67.56
97.62
4
A
ASP
47
-103.93
45.18
4
A
GLU
48
-49.94
106.96
4
A
PHE
56
35.00
47.98
4
A
ARG
76
-64.86
-178.98
4
A
LEU
81
-46.24
151.78
4
A
LEU
82
-166.23
110.78
5
A
VAL
9
-99.58
-60.75
5
A
SER
18
-56.92
177.65
5
A
ARG
22
40.04
25.62
5
A
THR
44
-65.30
88.81
5
A
ALA
45
-57.47
82.59
5
A
ASP
47
-102.61
73.01
5
A
PHE
56
37.51
41.05
5
A
GLU
66
-39.76
-25.51
5
A
CYS
67
-43.76
167.20
5
A
ASP
69
38.41
37.19
5
A
ARG
76
-55.98
174.16
5
A
LEU
82
-161.71
110.39
5
A
PRO
118
-69.75
87.15
5
A
PRO
127
-69.72
90.89
6
A
SER
3
39.00
43.58
6
A
SER
18
-65.26
-177.53
6
A
ASP
47
-117.82
74.24
6
A
PHE
56
36.66
41.44
6
A
CYS
67
-42.31
153.92
6
A
ASP
69
35.07
37.62
6
A
PRO
73
-69.75
-163.69
6
A
LEU
81
-46.39
153.39
6
A
LEU
82
-164.15
112.64
6
A
THR
115
-166.16
111.48
6
A
SER
125
-59.02
170.35
7
A
SER
2
-172.08
126.47
7
A
VAL
9
-97.57
-61.88
7
A
SER
18
-50.98
175.83
7
A
HIS
55
-43.17
108.76
7
A
PHE
56
36.84
47.99
7
A
ARG
76
-51.52
-174.95
7
A
LEU
81
-39.04
146.52
7
A
LEU
82
-162.67
110.97
7
A
PRO
118
-69.77
0.61
7
A
PRO
124
-69.79
-179.54
7
A
SER
128
-58.34
171.05
8
A
THR
44
-65.74
93.79
8
A
ALA
45
-56.98
95.99
8
A
GLU
48
-58.38
93.40
8
A
PHE
56
35.69
43.33
8
A
ARG
76
-58.08
172.10
8
A
LEU
81
-39.02
146.47
8
A
LEU
82
-163.13
110.37
8
A
PRO
118
-69.75
0.11
8
A
PRO
124
-69.79
-176.26
9
A
PHE
56
38.32
47.56
9
A
ARG
76
-51.11
-175.78
9
A
LEU
81
-38.79
142.84
9
A
THR
115
-166.79
112.05
9
A
PRO
116
-69.81
-170.96
9
A
PRO
118
-69.78
1.12
9
A
VAL
123
-171.19
136.61
10
A
SER
18
-67.37
-175.47
10
A
ARG
22
37.07
38.18
10
A
ALA
45
-65.59
87.48
10
A
GLN
46
-133.45
-46.49
10
A
PHE
56
36.14
48.29
10
A
GLU
66
-34.25
-36.74
10
A
CYS
67
-41.04
158.46
10
A
GLN
68
-114.41
-70.42
10
A
ARG
76
-68.92
-173.00
10
A
SER
90
-174.64
127.40
10
A
THR
115
-163.36
106.60
10
A
PRO
124
-69.78
1.33
10
A
PRO
127
-69.69
90.70
11
A
ARG
22
38.74
26.15
11
A
ALA
45
-78.48
49.60
11
A
ASP
47
-101.30
46.05
11
A
GLU
48
-34.44
113.50
11
A
PHE
56
37.18
35.15
11
A
CYS
67
-48.41
151.75
11
A
ARG
76
-55.03
-173.00
11
A
GLU
111
-74.70
-70.06
11
A
PRO
124
-69.80
95.62
12
A
SER
19
-101.29
-62.10
12
A
ARG
22
34.32
39.66
12
A
GLU
43
-39.23
-28.28
12
A
ALA
45
-85.62
47.15
12
A
ASP
47
-114.56
66.40
12
A
GLU
48
-54.54
107.44
12
A
PHE
56
38.23
45.59
12
A
GLN
68
-54.28
-175.27
12
A
ASP
69
-80.52
45.34
12
A
LEU
81
-35.08
143.65
12
A
LEU
82
-163.03
111.25
12
A
ALA
121
-59.46
100.81
12
A
THR
122
-83.79
40.25
12
A
PRO
124
-69.80
95.62
12
A
SER
128
-35.75
143.56
13
A
VAL
9
-127.55
-53.76
13
A
ALA
45
-81.34
47.83
13
A
ASP
47
-105.88
42.46
13
A
GLU
48
-35.44
123.29
13
A
PHE
56
39.36
47.16
13
A
PRO
73
-69.79
-168.61
13
A
ARG
76
-51.05
-176.03
13
A
LEU
81
-34.38
149.03
13
A
LEU
82
-161.44
112.23
13
A
THR
115
-161.05
105.06
14
A
SER
5
39.29
36.57
14
A
ASP
47
-106.70
76.59
14
A
PHE
56
35.88
45.32
14
A
GLN
65
-38.71
-39.66
14
A
PRO
73
-69.69
-178.31
14
A
ARG
76
-51.36
-175.13
14
A
GLU
88
-36.70
-34.16
14
A
SER
90
-166.08
116.69
14
A
PRO
116
-69.78
-177.11
14
A
SER
125
-92.59
-68.08
14
A
SER
128
-40.10
95.64
15
A
PHE
56
35.40
43.06
15
A
ARG
76
-52.35
-172.98
15
A
LEU
81
-38.19
138.42
15
A
SER
90
-171.11
145.93
15
A
PRO
116
-69.79
-176.79
15
A
PRO
124
-69.75
-171.21
15
A
PRO
127
-69.76
86.00
15
A
SER
129
-42.29
154.64
16
A
VAL
9
-94.70
-60.25
16
A
THR
44
-68.21
88.79
16
A
ALA
45
-55.58
88.80
16
A
GLN
46
-127.73
-50.00
16
A
GLU
48
-53.01
106.99
16
A
PHE
56
37.67
42.20
16
A
GLU
66
-34.46
-39.54
16
A
CYS
67
-37.09
149.09
16
A
GLN
68
-131.84
-64.21
16
A
PRO
73
-69.72
-168.73
16
A
PRO
124
-69.77
89.35
17
A
SER
5
-38.41
134.20
17
A
VAL
9
-95.74
-60.88
17
A
ARG
22
37.14
49.00
17
A
ALA
45
-46.31
91.99
17
A
GLU
48
-50.77
92.95
17
A
ASN
57
-130.66
-35.01
17
A
CYS
67
-35.07
124.55
17
A
PRO
73
-69.81
-164.76
17
A
ARG
76
-46.16
172.88
17
A
THR
115
-162.98
105.22
17
A
PRO
116
-69.78
-174.64
17
A
THR
122
-45.76
104.43
17
A
PRO
124
-69.76
1.11
17
A
SER
128
-46.13
152.81
18
A
GLU
43
-37.62
-39.49
18
A
GLU
66
-34.77
-36.96
18
A
CYS
67
-34.25
148.98
18
A
SER
90
-169.79
119.57
18
A
PRO
116
-69.77
-178.07
18
A
ALA
119
-57.09
175.91
18
A
ALA
121
-170.75
141.34
18
A
SER
129
-59.42
108.50
19
A
VAL
9
-94.61
-62.19
19
A
ARG
22
34.38
42.37
19
A
ASP
47
-109.65
44.60
19
A
GLU
48
-36.95
109.34
19
A
PHE
56
35.81
38.53
19
A
GLU
74
-54.90
108.67
19
A
THR
115
-160.51
107.82
19
A
PRO
116
-69.74
-173.26
19
A
ALA
121
71.90
36.38
20
A
ARG
22
34.41
47.82
20
A
ALA
45
-65.05
91.21
20
A
PHE
56
36.03
45.90
20
A
GLN
68
-58.54
-174.96
20
A
ASP
69
-82.03
39.72
20
A
GLU
74
-38.45
145.64
20
A
PRO
116
-69.67
-177.16
20
A
PRO
124
-69.77
98.09
Solution structure of the PH domain of Pleckstrin homology domain-containing protein family B member 1 from mouse
1
N
N
A
ARG
99
A
ARG
99
HELX_P
A
ASN
113
A
ASN
113
1
1
15
MEMBRANE PROTEIN
PH domain, PHRET1, structural genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, MEMBRANE PROTEIN
PLEB1_MOUSE
UNP
1
22
Q9QYE9
LVRGGWLWRQSSILRRWKRNWFALWLDGTLGYYHDETAQDEEDRVVIHFNVRDIKVGQECQDVQPPEGRSRDGLLTVNLR
EGSRLHLCAETRDDAIAWKTALMEANSTPAPAGATVP
22
138
2D9V
8
124
Q9QYE9
A
1
8
124
1
cloning artifact
GLY
1
2D9V
A
Q9QYE9
UNP
1
1
cloning artifact
SER
2
2D9V
A
Q9QYE9
UNP
2
1
cloning artifact
SER
3
2D9V
A
Q9QYE9
UNP
3
1
cloning artifact
GLY
4
2D9V
A
Q9QYE9
UNP
4
1
cloning artifact
SER
5
2D9V
A
Q9QYE9
UNP
5
1
cloning artifact
SER
6
2D9V
A
Q9QYE9
UNP
6
1
cloning artifact
GLY
7
2D9V
A
Q9QYE9
UNP
7
1
cloning artifact
SER
125
2D9V
A
Q9QYE9
UNP
125
1
cloning artifact
GLY
126
2D9V
A
Q9QYE9
UNP
126
1
cloning artifact
PRO
127
2D9V
A
Q9QYE9
UNP
127
1
cloning artifact
SER
128
2D9V
A
Q9QYE9
UNP
128
1
cloning artifact
SER
129
2D9V
A
Q9QYE9
UNP
129
1
cloning artifact
GLY
130
2D9V
A
Q9QYE9
UNP
130
7
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ASP
50
A
ASP
50
A
VAL
53
A
VAL
53
A
THR
36
A
THR
36
A
TYR
40
A
TYR
40
A
TRP
24
A
TRP
24
A
TRP
32
A
TRP
32
A
LEU
8
A
LEU
8
A
GLN
17
A
GLN
17
A
SER
90
A
SER
90
A
CYS
95
A
CYS
95
A
LEU
81
A
LEU
81
A
LEU
86
A
LEU
86
A
VAL
58
A
VAL
58
A
VAL
63
A
VAL
63