1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Feng, W.
Long, J.-F.
Chan, L.-N.
He, C.
Fu, A.
Xia, J.
Ip, N.Y.
Zhang, M.
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
US
Nat.Struct.Mol.Biol.
1545-9993
12
722
728
10.1038/nsmb958
16007100
Autoinhibition of X11/Mint scaffold proteins revealed by the closed conformation of the PDZ tandem
2005
10.2210/pdb1u39/pdb
pdb_00001u39
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
8720.254
amyloid beta A4 precursor protein-binding, family A, member 1
PDZ2 domain
1
man
polymer
X11alpha/Mint1, phosphotyrosine-binding/-interacting domain (PTB)-bearing protein, neuronal munc18-1-interacting protein 1, neuron-specific X11 protein, adaptor protein X11alpha
no
no
PPVTTVLIRRPDLRYQLGFSVQNGIICSLMRGGIAERGGVRVGHRIIEINGQSVVATPHEKIVHILSNAVGEIHMKTMPA
PPVTTVLIRRPDLRYQLGFSVQNGIICSLMRGGIAERGGVRVGHRIIEINGQSVVATPHEKIVHILSNAVGEIHMKTMPA
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
human
Homo
Escherichia
sample
9606
Homo sapiens
562
Escherichia coli
plasmid
pET32a
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2005-07-26
1
1
2007-10-21
1
2
2011-07-13
1
3
2022-03-02
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
The same protein, PDZ1 domain, 20 structures
The same protein complex with C-peptide, 20 structures
The same protein, PDZ12C domain, minimized average structure
RCSB
Y
PDBJ
2004-07-21
REL
REL
structures with the lowest energy
200
20
3D_15N-separated_NOESY
HNCO, HNCACB, CBCA(CO)NH
3D_13C-separated_NOESY
100mM potassium phosphate
6.5
1
atm
303
K
torsion angle dynamics
1
minimized average structure
1.0mM uniformly 15N labelled PDZ2 in 90% H2O, 10% D2O; 100mM potassium phosphate
90% H2O/10% D2O
1.0mM uniformly 15N/13C labelled PDZ2 in 90% H2O, 10% D2O; 100mM potassium phosphate
90% H2O/10% D2O
1.0mM uniformly 15N/13C labelled PDZ2 in 99.9% D2O; 100mM potassium phosphate
99.9% D2O
Brunger, A.T.
structure solution
CNS
1.1
Brunger, A.T.
refinement
CNS
1.1
750
Varian
INOVA
PRO
79
n
1
PRO
79
A
PRO
80
n
2
PRO
80
A
VAL
81
n
3
VAL
81
A
THR
82
n
4
THR
82
A
THR
83
n
5
THR
83
A
VAL
84
n
6
VAL
84
A
LEU
85
n
7
LEU
85
A
ILE
86
n
8
ILE
86
A
ARG
87
n
9
ARG
87
A
ARG
88
n
10
ARG
88
A
PRO
89
n
11
PRO
89
A
ASP
90
n
12
ASP
90
A
LEU
91
n
13
LEU
91
A
ARG
92
n
14
ARG
92
A
TYR
93
n
15
TYR
93
A
GLN
94
n
16
GLN
94
A
LEU
95
n
17
LEU
95
A
GLY
96
n
18
GLY
96
A
PHE
97
n
19
PHE
97
A
SER
98
n
20
SER
98
A
VAL
99
n
21
VAL
99
A
GLN
100
n
22
GLN
100
A
ASN
101
n
23
ASN
101
A
GLY
102
n
24
GLY
102
A
ILE
103
n
25
ILE
103
A
ILE
104
n
26
ILE
104
A
CYS
105
n
27
CYS
105
A
SER
106
n
28
SER
106
A
LEU
107
n
29
LEU
107
A
MET
108
n
30
MET
108
A
ARG
109
n
31
ARG
109
A
GLY
110
n
32
GLY
110
A
GLY
111
n
33
GLY
111
A
ILE
112
n
34
ILE
112
A
ALA
113
n
35
ALA
113
A
GLU
114
n
36
GLU
114
A
ARG
115
n
37
ARG
115
A
GLY
116
n
38
GLY
116
A
GLY
117
n
39
GLY
117
A
VAL
118
n
40
VAL
118
A
ARG
119
n
41
ARG
119
A
VAL
120
n
42
VAL
120
A
GLY
121
n
43
GLY
121
A
HIS
122
n
44
HIS
122
A
ARG
123
n
45
ARG
123
A
ILE
124
n
46
ILE
124
A
ILE
125
n
47
ILE
125
A
GLU
126
n
48
GLU
126
A
ILE
127
n
49
ILE
127
A
ASN
128
n
50
ASN
128
A
GLY
129
n
51
GLY
129
A
GLN
130
n
52
GLN
130
A
SER
131
n
53
SER
131
A
VAL
132
n
54
VAL
132
A
VAL
133
n
55
VAL
133
A
ALA
134
n
56
ALA
134
A
THR
135
n
57
THR
135
A
PRO
136
n
58
PRO
136
A
HIS
137
n
59
HIS
137
A
GLU
138
n
60
GLU
138
A
LYS
139
n
61
LYS
139
A
ILE
140
n
62
ILE
140
A
VAL
141
n
63
VAL
141
A
HIS
142
n
64
HIS
142
A
ILE
143
n
65
ILE
143
A
LEU
144
n
66
LEU
144
A
SER
145
n
67
SER
145
A
ASN
146
n
68
ASN
146
A
ALA
147
n
69
ALA
147
A
VAL
148
n
70
VAL
148
A
GLY
149
n
71
GLY
149
A
GLU
150
n
72
GLU
150
A
ILE
151
n
73
ILE
151
A
HIS
152
n
74
HIS
152
A
MET
153
n
75
MET
153
A
LYS
154
n
76
LYS
154
A
THR
155
n
77
THR
155
A
MET
156
n
78
MET
156
A
PRO
157
n
79
PRO
157
A
ALA
158
n
80
ALA
158
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
86
A
N
ILE
8
A
O
ILE
151
A
O
ILE
73
A
O
LYS
154
A
O
LYS
76
A
N
ILE
125
A
N
ILE
47
A
N
ILE
127
A
N
ILE
49
A
O
GLN
130
A
O
GLN
52
A
N
GLN
100
A
N
GLN
22
A
O
ILE
103
A
O
ILE
25
1
A
ASN
101
65.36
-68.51
1
A
CYS
105
-109.59
-71.68
1
A
ARG
109
-63.58
82.74
1
A
VAL
118
-37.59
114.92
1
A
VAL
120
-48.11
101.76
1
A
ILE
125
-151.54
-84.51
1
A
ASN
128
59.84
18.64
1
A
ALA
147
-103.62
79.21
2
A
LEU
91
-96.19
30.87
2
A
CYS
105
-108.00
-65.62
2
A
ARG
109
-67.97
71.92
2
A
VAL
118
-29.58
-64.26
2
A
ARG
119
61.71
178.70
2
A
ILE
125
-137.18
-84.46
3
A
ASN
101
64.34
-68.19
3
A
CYS
105
-106.46
-79.48
3
A
LEU
107
-174.16
101.86
3
A
ARG
109
-66.03
78.20
3
A
VAL
118
-15.11
-83.31
3
A
ARG
119
62.56
143.19
3
A
ILE
125
-157.79
-86.66
3
A
PRO
136
-47.92
164.09
4
A
PHE
97
-175.55
145.14
4
A
CYS
105
-94.97
-67.35
4
A
ARG
109
-93.40
44.14
4
A
VAL
118
-34.13
148.80
4
A
ILE
125
-128.29
-84.46
4
A
ALA
147
-118.06
52.59
4
A
VAL
148
-53.50
-178.48
5
A
PRO
80
-52.05
88.87
5
A
ASP
90
-127.50
-169.17
5
A
CYS
105
-94.29
-84.28
5
A
ARG
109
-63.89
80.79
5
A
VAL
118
-15.72
-81.98
5
A
ARG
119
63.84
129.05
5
A
ILE
125
-146.07
-84.50
5
A
PRO
136
-49.72
156.97
6
A
ASN
101
64.69
-70.66
6
A
ARG
109
-55.21
91.00
6
A
ILE
125
-147.14
-83.02
6
A
PRO
157
-50.92
109.38
7
A
LEU
95
-96.98
-61.35
7
A
PHE
97
-176.68
-171.96
7
A
ASN
101
65.18
-64.64
7
A
CYS
105
-105.42
-77.73
7
A
VAL
118
-31.75
145.72
7
A
ILE
125
-149.38
-82.99
7
A
PRO
136
-42.77
164.20
7
A
ALA
147
-116.98
58.19
7
A
VAL
148
-53.28
173.70
8
A
PRO
80
-66.64
62.57
8
A
ASN
101
64.94
-67.16
8
A
CYS
105
-97.81
-80.11
8
A
ARG
109
-90.87
47.52
8
A
VAL
118
-31.87
116.56
8
A
VAL
120
-46.99
108.42
8
A
ILE
125
-141.42
-84.79
8
A
ALA
147
-116.82
56.39
8
A
VAL
148
-54.21
-177.96
9
A
ASN
101
63.89
-73.94
9
A
CYS
105
-105.59
-67.54
9
A
ARG
109
-68.70
72.21
9
A
VAL
118
-38.50
129.47
9
A
ILE
125
-154.79
-85.04
9
A
PRO
136
-48.27
164.16
9
A
VAL
148
44.44
-173.63
10
A
ASN
101
56.59
18.97
10
A
CYS
105
-108.89
-75.39
10
A
ARG
109
-91.96
45.53
10
A
VAL
118
-35.49
153.19
10
A
ILE
124
-46.16
156.70
10
A
ILE
125
-153.89
-86.06
10
A
ASN
128
48.18
26.51
10
A
ALA
147
-117.62
59.52
10
A
VAL
148
-54.74
175.70
11
A
CYS
105
-106.15
-72.18
11
A
ARG
109
-93.25
44.47
11
A
VAL
118
-24.91
136.87
11
A
VAL
120
-57.11
100.21
11
A
ILE
125
-148.59
-84.71
11
A
VAL
148
44.86
-171.38
12
A
GLN
94
-66.42
-177.83
12
A
ASN
101
58.26
18.91
12
A
SER
106
-178.19
141.24
12
A
ARG
109
-58.81
86.49
12
A
VAL
118
-31.25
102.04
12
A
VAL
120
-53.76
99.99
12
A
ILE
124
-48.09
157.85
12
A
ILE
125
-150.73
-83.37
12
A
VAL
148
45.96
-174.68
13
A
CYS
105
-116.82
-81.10
13
A
ARG
109
-66.13
76.71
13
A
VAL
118
-26.43
123.70
13
A
VAL
120
-52.20
93.23
13
A
ILE
125
-147.45
-84.31
14
A
PRO
80
-69.76
85.77
14
A
ASP
90
-173.07
-169.38
14
A
CYS
105
-126.51
-80.64
14
A
VAL
118
-37.95
135.90
14
A
VAL
120
-57.11
89.45
14
A
ILE
125
-150.77
-85.66
14
A
VAL
148
57.01
164.61
15
A
ARG
88
-164.57
97.81
15
A
ASN
101
57.78
18.28
15
A
CYS
105
-105.00
-77.98
15
A
MET
108
-68.13
98.26
15
A
VAL
118
-34.27
146.36
15
A
ILE
124
-49.98
158.21
15
A
ILE
125
-148.99
-82.70
15
A
VAL
148
44.56
-172.67
16
A
LEU
95
-93.61
-67.62
16
A
PHE
97
179.96
177.41
16
A
LEU
107
-167.25
116.46
16
A
VAL
118
-30.76
147.24
16
A
VAL
120
-62.00
95.75
16
A
HIS
122
-125.32
-165.98
16
A
ILE
125
-150.31
-84.48
16
A
ALA
147
-117.89
54.88
16
A
VAL
148
-50.78
177.61
17
A
TYR
93
-60.30
-177.44
17
A
ASN
101
57.11
18.74
17
A
CYS
105
-106.44
-69.89
17
A
ARG
109
-65.05
78.88
17
A
VAL
118
-30.34
144.58
17
A
VAL
120
-56.05
90.79
17
A
ILE
125
-137.97
-82.84
17
A
ALA
147
-119.26
63.45
17
A
VAL
148
-60.11
-157.28
18
A
ASN
101
58.25
17.25
18
A
CYS
105
-84.62
-75.62
18
A
ARG
109
-67.18
76.14
18
A
VAL
118
-29.75
-71.46
18
A
ARG
119
64.32
136.12
18
A
ILE
125
-137.11
-84.80
18
A
ASN
128
57.82
17.87
18
A
PRO
136
-49.65
164.04
18
A
ALA
147
-118.65
55.26
18
A
VAL
148
-55.84
174.89
19
A
TYR
93
-56.69
174.72
19
A
ASN
101
59.67
18.04
19
A
LEU
107
-162.26
116.54
19
A
ARG
109
-65.44
79.50
19
A
VAL
118
-40.46
108.21
19
A
VAL
120
-54.06
92.61
19
A
ILE
125
-136.65
-83.98
20
A
PRO
80
-51.73
90.03
20
A
LEU
95
-91.42
-66.67
20
A
CYS
105
-100.52
-78.79
20
A
VAL
118
-34.70
128.07
20
A
ILE
124
-49.71
159.14
20
A
ILE
125
-148.79
-82.23
minimized average
Auto-inhibition Mechanism of X11s/Mints Family Scaffold Proteins Revealed by the Closed Conformation of the Tandem PDZ Domains
1
N
N
A
ILE
112
A
ILE
34
HELX_P
A
GLY
117
A
GLY
39
1
1
6
A
VAL
133
A
VAL
55
HELX_P
A
THR
135
A
THR
57
5
2
3
A
PRO
136
A
PRO
58
HELX_P
A
ASN
146
A
ASN
68
1
3
11
PROTEIN TRANSPORT
X11s/Mints, PDZ domain, scaffold protein, protein trafficking, PROTEIN TRANSPORT
APBA1_HUMAN
UNP
1
743
Q02410
PPVTTVLIRRPDLRYQLGFSVQNGIICSLMRGGIAERGGVRVGHRIIEINGQSVVATPHEKIVHILSNAVGEIHMKTMPA
743
822
1U39
79
158
Q02410
A
1
1
80
4
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
THR
82
A
THR
4
A
ARG
87
A
ARG
9
A
GLU
150
A
GLU
72
A
MET
156
A
MET
78
A
ARG
123
A
ARG
45
A
ILE
127
A
ILE
49
A
GLN
130
A
GLN
52
A
SER
131
A
SER
53
A
PHE
97
A
PHE
19
A
GLN
100
A
GLN
22
A
ILE
103
A
ILE
25
A
LEU
107
A
LEU
29