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.
Suetake, 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
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 PDZ domain of human Rho guanine nucleotide exchange factor 11
10.2210/pdb2dls/pdb
pdb_00002dls
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
9441.792
Rho guanine nucleotide exchange factor 11
PDZ domain
1
man
polymer
PDZ-RhoGEF
no
no
GSSGSSGVQRCVIIQKDQHGFGFTVSGDRIVLVQSVRPGGAAMKAGVKEGDRIIKVNGTMVTNSSHLEVVKLIKSGAYVA
LTLLGSSSGPSSG
GSSGSSGVQRCVIIQKDQHGFGFTVSGDRIVLVQSVRPGGAAMKAGVKEGDRIIKVNGTMVTNSSHLEVVKLIKSGAYVA
LTLLGSSSGPSSG
A
hsk002000370.1
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
human
Homo
sample
Cell-free protein synthesis
ARHGEF11, KIAA0380
9606
Homo sapiens
Cell free synthesis
PLASMID
P050919-12
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
Version format compliance
Data collection
Database references
Derived calculations
1
0
2006-10-20
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
_struct_ref_seq_dif.details
HELIX
Determination method: Author determined
Y
PDBJ
Y
PDBJ
2006-04-20
REL
target function, structures with the lowest energy, structures with the least restraint violations
100
20
3D_15N-separated_NOESY
3D_13C-separated_NOESY
120mM
7.0
ambient
293
K
torsion angle dynamics
1
lowest energy
1.20mM 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
Varian
collection
VNMR
6.1C
Delaglio, F.
processing
NMRPipe
20031121
Johnson, B.A.
data analysis
NMRView
5.0.4
Kobayashi, N.
data analysis
KUJIRA
0.93191
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
VAL
8
n
8
VAL
8
A
GLN
9
n
9
GLN
9
A
ARG
10
n
10
ARG
10
A
CYS
11
n
11
CYS
11
A
VAL
12
n
12
VAL
12
A
ILE
13
n
13
ILE
13
A
ILE
14
n
14
ILE
14
A
GLN
15
n
15
GLN
15
A
LYS
16
n
16
LYS
16
A
ASP
17
n
17
ASP
17
A
GLN
18
n
18
GLN
18
A
HIS
19
n
19
HIS
19
A
GLY
20
n
20
GLY
20
A
PHE
21
n
21
PHE
21
A
GLY
22
n
22
GLY
22
A
PHE
23
n
23
PHE
23
A
THR
24
n
24
THR
24
A
VAL
25
n
25
VAL
25
A
SER
26
n
26
SER
26
A
GLY
27
n
27
GLY
27
A
ASP
28
n
28
ASP
28
A
ARG
29
n
29
ARG
29
A
ILE
30
n
30
ILE
30
A
VAL
31
n
31
VAL
31
A
LEU
32
n
32
LEU
32
A
VAL
33
n
33
VAL
33
A
GLN
34
n
34
GLN
34
A
SER
35
n
35
SER
35
A
VAL
36
n
36
VAL
36
A
ARG
37
n
37
ARG
37
A
PRO
38
n
38
PRO
38
A
GLY
39
n
39
GLY
39
A
GLY
40
n
40
GLY
40
A
ALA
41
n
41
ALA
41
A
ALA
42
n
42
ALA
42
A
MET
43
n
43
MET
43
A
LYS
44
n
44
LYS
44
A
ALA
45
n
45
ALA
45
A
GLY
46
n
46
GLY
46
A
VAL
47
n
47
VAL
47
A
LYS
48
n
48
LYS
48
A
GLU
49
n
49
GLU
49
A
GLY
50
n
50
GLY
50
A
ASP
51
n
51
ASP
51
A
ARG
52
n
52
ARG
52
A
ILE
53
n
53
ILE
53
A
ILE
54
n
54
ILE
54
A
LYS
55
n
55
LYS
55
A
VAL
56
n
56
VAL
56
A
ASN
57
n
57
ASN
57
A
GLY
58
n
58
GLY
58
A
THR
59
n
59
THR
59
A
MET
60
n
60
MET
60
A
VAL
61
n
61
VAL
61
A
THR
62
n
62
THR
62
A
ASN
63
n
63
ASN
63
A
SER
64
n
64
SER
64
A
SER
65
n
65
SER
65
A
HIS
66
n
66
HIS
66
A
LEU
67
n
67
LEU
67
A
GLU
68
n
68
GLU
68
A
VAL
69
n
69
VAL
69
A
VAL
70
n
70
VAL
70
A
LYS
71
n
71
LYS
71
A
LEU
72
n
72
LEU
72
A
ILE
73
n
73
ILE
73
A
LYS
74
n
74
LYS
74
A
SER
75
n
75
SER
75
A
GLY
76
n
76
GLY
76
A
ALA
77
n
77
ALA
77
A
TYR
78
n
78
TYR
78
A
VAL
79
n
79
VAL
79
A
ALA
80
n
80
ALA
80
A
LEU
81
n
81
LEU
81
A
THR
82
n
82
THR
82
A
LEU
83
n
83
LEU
83
A
LEU
84
n
84
LEU
84
A
GLY
85
n
85
GLY
85
A
SER
86
n
86
SER
86
A
SER
87
n
87
SER
87
A
SER
88
n
88
SER
88
A
GLY
89
n
89
GLY
89
A
PRO
90
n
90
PRO
90
A
SER
91
n
91
SER
91
A
SER
92
n
92
SER
92
A
GLY
93
n
93
GLY
93
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
81
A
O
LEU
81
A
O
THR
82
A
O
THR
82
A
N
ILE
54
A
N
ILE
54
A
N
VAL
56
A
N
VAL
56
A
O
THR
59
A
O
THR
59
A
N
THR
24
A
N
THR
24
A
O
GLN
34
A
O
GLN
34
1
A
SER
5
-40.90
109.95
1
A
GLN
18
-112.37
61.26
1
A
SER
26
-171.00
129.54
1
A
ASP
28
-73.89
-70.90
1
A
VAL
33
-58.67
109.34
1
A
SER
64
-39.08
158.30
2
A
SER
2
37.62
42.48
2
A
PHE
21
-35.97
151.28
2
A
SER
26
-172.42
141.31
2
A
SER
86
-43.97
155.16
2
A
SER
88
-36.05
123.69
2
A
PRO
90
-69.79
95.30
3
A
LYS
16
-35.46
148.59
3
A
ARG
37
-36.72
142.05
3
A
PRO
38
-69.76
89.50
3
A
ASN
63
-118.64
65.53
4
A
GLN
18
-38.45
-31.53
4
A
VAL
33
-46.41
106.54
4
A
ARG
37
-38.65
140.64
4
A
SER
75
-50.31
92.44
5
A
SER
3
-171.11
134.53
5
A
ASP
17
-131.49
-40.60
5
A
GLN
18
-118.27
65.08
5
A
ASP
28
-63.83
-70.17
5
A
PRO
38
-69.75
82.19
5
A
SER
64
-42.65
159.52
5
A
LYS
74
-95.66
58.56
5
A
SER
91
-47.26
160.42
6
A
GLN
18
-134.99
-67.23
6
A
ASP
28
-79.28
-74.84
6
A
PRO
38
-69.77
99.29
6
A
ALA
41
-124.33
-50.67
6
A
ASN
63
71.05
33.51
7
A
GLN
18
-109.35
42.79
7
A
ARG
29
-106.48
-68.36
7
A
ARG
37
-34.96
139.84
7
A
PRO
38
-69.78
88.47
7
A
VAL
61
-97.41
34.00
7
A
SER
64
-43.90
150.78
8
A
LYS
16
-38.91
137.22
8
A
ASP
17
-107.57
-70.76
8
A
THR
62
-132.03
-36.22
8
A
LYS
74
-95.49
53.22
9
A
SER
3
-99.26
-61.93
9
A
SER
5
-38.11
131.81
9
A
SER
26
-173.68
144.17
9
A
PRO
90
-69.75
91.28
10
A
GLN
18
-98.76
47.51
10
A
PRO
38
-69.81
94.37
10
A
VAL
61
-92.52
39.24
10
A
LYS
71
-34.73
-39.99
10
A
LYS
74
-90.49
46.74
10
A
PRO
90
-69.80
89.04
10
A
SER
92
-109.81
42.75
11
A
SER
3
-51.94
94.97
11
A
GLN
18
70.59
36.93
11
A
ASP
28
-77.84
-71.07
11
A
ARG
29
-71.14
-75.08
11
A
ARG
37
-36.77
136.69
11
A
PRO
38
-69.75
88.69
11
A
SER
64
-43.78
161.64
11
A
LYS
74
-42.68
-72.01
11
A
SER
75
-47.64
106.56
11
A
SER
88
36.76
51.00
12
A
PHE
21
-65.25
-176.86
12
A
ILE
30
-102.01
76.54
12
A
VAL
31
-32.88
105.01
13
A
SER
6
-68.17
88.71
13
A
ASP
28
-70.85
-70.45
13
A
VAL
33
-58.24
102.55
13
A
LYS
74
-94.81
43.72
14
A
LYS
16
-59.30
170.55
14
A
PHE
21
-51.63
170.64
14
A
ILE
30
-108.91
78.84
14
A
SER
64
-37.10
154.34
14
A
LEU
67
-38.00
-36.76
15
A
SER
3
-57.50
171.93
15
A
LYS
16
-34.62
118.13
15
A
HIS
19
38.23
42.64
15
A
PHE
21
-49.98
168.18
15
A
VAL
31
-35.22
97.89
15
A
VAL
33
-57.56
108.91
15
A
PRO
38
-69.81
90.03
15
A
HIS
66
-69.51
-70.24
15
A
SER
88
-63.88
74.61
16
A
SER
5
36.79
43.71
16
A
PHE
21
-45.37
164.68
16
A
VAL
31
-49.43
107.27
16
A
ARG
37
-38.22
134.61
16
A
PRO
38
-69.78
99.58
16
A
ALA
41
-120.93
-52.49
16
A
MET
60
-59.15
104.97
16
A
HIS
66
-40.56
-71.98
16
A
GLU
68
-39.24
-38.66
17
A
ASP
28
-175.07
-179.19
17
A
VAL
31
-33.19
128.38
17
A
ARG
37
-36.61
139.56
17
A
PRO
38
-69.73
90.17
17
A
LYS
71
-36.66
-32.97
17
A
LYS
74
-41.44
-73.57
17
A
SER
75
-42.04
103.69
17
A
SER
88
-34.65
127.00
17
A
PRO
90
-69.77
2.70
18
A
LYS
16
-34.47
107.87
18
A
GLN
18
-111.66
50.39
18
A
PHE
21
-56.05
174.60
18
A
ASP
28
-76.18
-75.19
18
A
ARG
29
-62.70
-73.36
18
A
ARG
37
-36.06
135.97
18
A
PRO
38
-69.74
82.48
18
A
ASN
57
48.90
29.12
18
A
SER
87
-130.79
-61.15
18
A
SER
88
-50.83
103.11
18
A
PRO
90
-69.82
95.66
19
A
SER
2
35.29
40.96
19
A
SER
5
-121.02
-59.10
19
A
PRO
38
-69.71
3.61
19
A
SER
75
-44.92
102.11
19
A
SER
91
-34.55
131.02
20
A
SER
3
-172.67
140.25
20
A
SER
5
-132.47
-48.27
20
A
ASP
28
-75.35
-70.85
20
A
ARG
29
-66.11
-70.68
20
A
ARG
37
-37.90
135.04
20
A
SER
64
-51.98
-176.79
20
A
LYS
74
-65.53
-71.86
20
A
SER
75
-37.48
107.09
20
A
ALA
77
-35.67
-34.70
Solution structure of the PDZ domain of human Rho guanine nucleotide exchange factor 11
1
N
N
A
ALA
42
A
ALA
42
HELX_P
A
ALA
45
A
ALA
45
1
1
4
A
SER
65
A
SER
65
HELX_P
A
LYS
74
A
LYS
74
1
2
10
SIGNALING PROTEIN
PDZ domain, Rho guanine nucleotide exchange factor 11, PDZ-RhoGEF, ARHGEF11, KIAA0380, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, SIGNALING PROTEIN
ARHGB_HUMAN
UNP
1
44
O15085
44
123
2DLS
8
87
O15085
A
1
8
87
1
cloning artifact
GLY
1
2DLS
A
O15085
UNP
1
1
cloning artifact
SER
2
2DLS
A
O15085
UNP
2
1
cloning artifact
SER
3
2DLS
A
O15085
UNP
3
1
cloning artifact
GLY
4
2DLS
A
O15085
UNP
4
1
cloning artifact
SER
5
2DLS
A
O15085
UNP
5
1
cloning artifact
SER
6
2DLS
A
O15085
UNP
6
1
cloning artifact
GLY
7
2DLS
A
O15085
UNP
7
1
cloning artifact
SER
88
2DLS
A
O15085
UNP
88
1
cloning artifact
GLY
89
2DLS
A
O15085
UNP
89
1
cloning artifact
PRO
90
2DLS
A
O15085
UNP
90
1
cloning artifact
SER
91
2DLS
A
O15085
UNP
91
1
cloning artifact
SER
92
2DLS
A
O15085
UNP
92
1
cloning artifact
GLY
93
2DLS
A
O15085
UNP
93
4
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
GLN
9
A
GLN
9
A
GLN
15
A
GLN
15
A
TYR
78
A
TYR
78
A
LEU
84
A
LEU
84
A
ARG
52
A
ARG
52
A
VAL
56
A
VAL
56
A
THR
59
A
THR
59
A
MET
60
A
MET
60
A
PHE
23
A
PHE
23
A
SER
26
A
SER
26
A
LEU
32
A
LEU
32
A
VAL
36
A
VAL
36