1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Lu, J.
Garcia, J.
Dulubova, I.
Sudhof, T.C.
Rizo, J.
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
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
US
Biochemistry
BICHAW
0033
0006-2960
41
5956
5962
10.1021/bi020050b
11993989
Solution structure of the Vam7p PX domain.
2002
10.2210/pdb1kmd/pdb
pdb_00001kmd
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
14418.483
Vacuolar morphogenesis protein VAM7
PX domain, Residues 8-124
1
man
polymer
Vam7p
no
no
KMSEKLRIKVDDVKINPKYVLYGVSTPNKRLYKRYSEFWKLKTRLERDVGSTIPYDFPEKPGVLDRRWQRRYDDPEMIDE
RRIGLERFLNELYNDRFDSRWRDTKIAQDFLQLSKPN
KMSEKLRIKVDDVKINPKYVLYGVSTPNKRLYKRYSEFWKLKTRLERDVGSTIPYDFPEKPGVLDRRWQRRYDDPEMIDE
RRIGLERFLNELYNDRFDSRWRDTKIAQDFLQLSKPN
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
n
n
n
n
n
n
n
baker's yeast
Saccharomyces
Escherichia
Escherichia coli
sample
4932
Saccharomyces cerevisiae
511693
Escherichia coli BL21
BL21
PLASMID
pGEX-KG
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2002-06-12
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RCSB
Y
RCSB
2001-12-14
REL
REL
The structure was determined using triple-resonance NMR spectroscopy.
STRUCTURES WITH THE MINIMAL NOE ENERGY
500
20
3D_15N-separated_NOESY
3D_13C-separated_NOESY
20mM Mes
6.2
1
atm
298
K
the structures are based on a total of 1443 restraints, 1193 are NOE-derived
distance constraints, 152 dihedral angle restraints, 98 distance restraints
from hydrogen bonds.
torsion angle dynamics
1
0.5mM Vam7p PX domain U-15N,20mM Mes buffer
90% H2O/10% D2O
0.5mM Vam7p PX domain U-15N, 13C, 20mM Mes buffer
90% H2O/10% D2O
0.5mM Vam7p PX domain U-15N, 20mM Mes Buffer
100% D2O
0.5mM Vam7p PX domain 10%-13C, 20mM Mes buffer
90% H2O/10% D2O
DeLaglio, F. et al.
processing
NMRPipe
1.8
Varian
collection
VNMR
6.1
Johnson, B. and Blevins R.
data analysis
NMRView
4.1.2
Brunger, A.T. et al.
refinement
CNS
1.0
500
Varian
INOVA
600
Varian
INOVA
LYS
8
n
1
LYS
8
A
MET
9
n
2
MET
9
A
SER
10
n
3
SER
10
A
GLU
11
n
4
GLU
11
A
LYS
12
n
5
LYS
12
A
LEU
13
n
6
LEU
13
A
ARG
14
n
7
ARG
14
A
ILE
15
n
8
ILE
15
A
LYS
16
n
9
LYS
16
A
VAL
17
n
10
VAL
17
A
ASP
18
n
11
ASP
18
A
ASP
19
n
12
ASP
19
A
VAL
20
n
13
VAL
20
A
LYS
21
n
14
LYS
21
A
ILE
22
n
15
ILE
22
A
ASN
23
n
16
ASN
23
A
PRO
24
n
17
PRO
24
A
LYS
25
n
18
LYS
25
A
TYR
26
n
19
TYR
26
A
VAL
27
n
20
VAL
27
A
LEU
28
n
21
LEU
28
A
TYR
29
n
22
TYR
29
A
GLY
30
n
23
GLY
30
A
VAL
31
n
24
VAL
31
A
SER
32
n
25
SER
32
A
THR
33
n
26
THR
33
A
PRO
34
n
27
PRO
34
A
ASN
35
n
28
ASN
35
A
LYS
36
n
29
LYS
36
A
ARG
37
n
30
ARG
37
A
LEU
38
n
31
LEU
38
A
TYR
39
n
32
TYR
39
A
LYS
40
n
33
LYS
40
A
ARG
41
n
34
ARG
41
A
TYR
42
n
35
TYR
42
A
SER
43
n
36
SER
43
A
GLU
44
n
37
GLU
44
A
PHE
45
n
38
PHE
45
A
TRP
46
n
39
TRP
46
A
LYS
47
n
40
LYS
47
A
LEU
48
n
41
LEU
48
A
LYS
49
n
42
LYS
49
A
THR
50
n
43
THR
50
A
ARG
51
n
44
ARG
51
A
LEU
52
n
45
LEU
52
A
GLU
53
n
46
GLU
53
A
ARG
54
n
47
ARG
54
A
ASP
55
n
48
ASP
55
A
VAL
56
n
49
VAL
56
A
GLY
57
n
50
GLY
57
A
SER
58
n
51
SER
58
A
THR
59
n
52
THR
59
A
ILE
60
n
53
ILE
60
A
PRO
61
n
54
PRO
61
A
TYR
62
n
55
TYR
62
A
ASP
63
n
56
ASP
63
A
PHE
64
n
57
PHE
64
A
PRO
65
n
58
PRO
65
A
GLU
66
n
59
GLU
66
A
LYS
67
n
60
LYS
67
A
PRO
68
n
61
PRO
68
A
GLY
69
n
62
GLY
69
A
VAL
70
n
63
VAL
70
A
LEU
71
n
64
LEU
71
A
ASP
72
n
65
ASP
72
A
ARG
73
n
66
ARG
73
A
ARG
74
n
67
ARG
74
A
TRP
75
n
68
TRP
75
A
GLN
76
n
69
GLN
76
A
ARG
77
n
70
ARG
77
A
ARG
78
n
71
ARG
78
A
TYR
79
n
72
TYR
79
A
ASP
80
n
73
ASP
80
A
ASP
81
n
74
ASP
81
A
PRO
82
n
75
PRO
82
A
GLU
83
n
76
GLU
83
A
MET
84
n
77
MET
84
A
ILE
85
n
78
ILE
85
A
ASP
86
n
79
ASP
86
A
GLU
87
n
80
GLU
87
A
ARG
88
n
81
ARG
88
A
ARG
89
n
82
ARG
89
A
ILE
90
n
83
ILE
90
A
GLY
91
n
84
GLY
91
A
LEU
92
n
85
LEU
92
A
GLU
93
n
86
GLU
93
A
ARG
94
n
87
ARG
94
A
PHE
95
n
88
PHE
95
A
LEU
96
n
89
LEU
96
A
ASN
97
n
90
ASN
97
A
GLU
98
n
91
GLU
98
A
LEU
99
n
92
LEU
99
A
TYR
100
n
93
TYR
100
A
ASN
101
n
94
ASN
101
A
ASP
102
n
95
ASP
102
A
ARG
103
n
96
ARG
103
A
PHE
104
n
97
PHE
104
A
ASP
105
n
98
ASP
105
A
SER
106
n
99
SER
106
A
ARG
107
n
100
ARG
107
A
TRP
108
n
101
TRP
108
A
ARG
109
n
102
ARG
109
A
ASP
110
n
103
ASP
110
A
THR
111
n
104
THR
111
A
LYS
112
n
105
LYS
112
A
ILE
113
n
106
ILE
113
A
ALA
114
n
107
ALA
114
A
GLN
115
n
108
GLN
115
A
ASP
116
n
109
ASP
116
A
PHE
117
n
110
PHE
117
A
LEU
118
n
111
LEU
118
A
GLN
119
n
112
GLN
119
A
LEU
120
n
113
LEU
120
A
SER
121
n
114
SER
121
A
LYS
122
n
115
LYS
122
A
PRO
123
n
116
PRO
123
A
ASN
124
n
117
ASN
124
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
LEU
38
A
O
LEU
31
A
N
VAL
31
A
N
VAL
24
A
O
SER
32
A
O
SER
25
A
N
LYS
16
A
N
LYS
9
A
O
LEU
38
A
O
LEU
31
A
N
VAL
31
A
N
VAL
24
A
O
LEU
28
A
O
LEU
21
A
N
LYS
21
A
N
LYS
14
1
A
ASP
18
-144.25
27.76
1
A
LYS
36
167.70
-176.56
1
A
LYS
49
-63.11
-73.96
1
A
PRO
61
-88.50
34.05
1
A
VAL
70
-81.43
-78.81
1
A
LEU
71
-156.32
39.40
1
A
ARG
103
-133.33
-62.28
1
A
LEU
120
-92.35
38.06
1
A
SER
121
-74.23
-168.36
2
A
ARG
14
-65.10
98.88
2
A
ASP
18
-142.69
25.62
2
A
LYS
36
165.52
-179.13
2
A
LYS
49
-55.09
-71.48
2
A
VAL
70
-77.37
-79.41
2
A
ASN
101
-90.48
52.54
2
A
ARG
103
-122.84
-67.45
2
A
LEU
120
-91.76
38.76
3
A
LYS
36
136.16
-178.34
3
A
LYS
49
-62.09
-72.80
3
A
PRO
61
-88.61
35.11
3
A
VAL
70
-103.20
-79.16
3
A
LEU
71
-107.11
57.95
3
A
LEU
120
-92.30
38.15
3
A
SER
121
-105.40
-163.62
4
A
LYS
36
166.59
-179.41
4
A
LYS
49
-56.17
-70.27
4
A
PRO
61
-86.09
34.95
4
A
VAL
70
-98.17
-78.98
4
A
ARG
73
-141.67
13.44
4
A
ASN
101
-95.41
57.43
4
A
LEU
120
-92.03
38.59
5
A
LYS
36
167.86
-178.37
5
A
LYS
49
-55.45
-72.51
5
A
PRO
61
-85.52
33.94
5
A
VAL
70
-67.37
-79.47
5
A
LEU
71
-114.33
70.16
5
A
ASN
101
-94.17
52.25
5
A
LEU
120
-93.92
40.45
6
A
ASP
18
-155.42
26.58
6
A
LYS
36
169.18
177.40
6
A
LYS
49
-52.54
-72.31
6
A
GLU
66
-74.73
-167.16
6
A
VAL
70
-124.35
-79.16
6
A
LEU
71
-166.70
45.52
6
A
ASP
80
-98.90
33.67
6
A
ARG
103
-128.64
-50.53
6
A
LEU
120
-90.66
37.48
6
A
SER
121
57.11
176.40
7
A
LYS
36
168.30
-178.30
7
A
PRO
61
-87.97
32.58
7
A
VAL
70
-124.31
-78.99
7
A
ARG
73
-135.86
-43.06
7
A
GLN
76
60.19
151.12
7
A
ASN
101
-95.34
47.56
7
A
ARG
103
-112.52
-78.33
7
A
LEU
120
-87.29
39.31
8
A
LYS
36
166.62
-178.09
8
A
LYS
49
-58.97
-72.69
8
A
PRO
61
-87.11
31.05
8
A
VAL
70
-60.57
-78.72
8
A
LEU
99
-90.04
-60.69
8
A
LEU
120
-94.40
41.80
8
A
SER
121
-175.04
-166.41
9
A
ASP
18
-151.90
26.08
9
A
LYS
36
105.99
-169.12
9
A
LYS
49
-56.33
-72.39
9
A
PRO
61
-87.03
38.13
9
A
VAL
70
-91.01
-79.26
9
A
LEU
71
-97.41
42.80
9
A
LEU
120
-89.44
33.83
10
A
ASP
18
-141.24
30.42
10
A
LYS
36
167.59
-177.61
10
A
LYS
49
-59.25
-70.88
10
A
VAL
70
-90.19
-78.21
10
A
LEU
71
-93.82
41.62
10
A
ARG
74
-158.58
-59.41
10
A
ASN
101
-89.71
48.62
10
A
LEU
120
-93.35
41.13
11
A
LYS
36
169.75
-179.11
11
A
LYS
49
-73.39
-71.04
11
A
PRO
61
-87.13
42.40
11
A
LEU
71
80.15
53.63
11
A
ARG
73
-141.00
-55.94
11
A
LEU
120
-92.74
38.41
12
A
ASP
18
-143.90
24.71
12
A
LYS
36
168.73
-178.45
12
A
LYS
49
-50.50
-70.80
12
A
PRO
61
-84.79
43.41
12
A
VAL
70
-100.56
-79.23
12
A
ARG
73
-160.89
-43.89
12
A
ASN
101
-94.46
45.21
12
A
LEU
120
-97.32
37.03
13
A
ASP
18
-142.73
23.50
13
A
LYS
36
136.76
-179.57
13
A
LYS
49
-56.01
-70.92
13
A
PRO
61
-86.02
39.33
13
A
VAL
70
-75.82
-78.98
13
A
ARG
73
-137.92
-44.98
13
A
LEU
99
-90.87
-60.43
13
A
ARG
103
-120.51
-50.39
13
A
LEU
120
-90.16
40.66
13
A
SER
121
-70.61
-163.30
14
A
LYS
36
168.90
-177.00
14
A
LYS
49
-54.43
-72.06
14
A
VAL
70
-94.29
-78.93
14
A
ARG
73
-157.41
-43.94
14
A
ASP
80
-97.11
34.07
14
A
LEU
120
-94.23
42.04
15
A
LYS
36
167.76
-177.41
15
A
LYS
49
-57.44
-75.01
15
A
PRO
61
-87.31
32.01
15
A
VAL
70
-77.02
-78.84
15
A
ARG
73
176.88
-36.59
15
A
ARG
103
-127.10
-73.19
15
A
LEU
120
-90.31
39.70
16
A
LYS
36
99.75
-167.57
16
A
LYS
49
-55.73
-72.20
16
A
VAL
70
-93.08
-78.90
16
A
LEU
71
-103.23
56.89
16
A
ARG
73
-133.87
-61.39
16
A
LEU
120
-93.72
41.28
17
A
LYS
36
137.00
-175.87
17
A
LYS
49
-54.06
-71.40
17
A
PRO
61
-88.34
34.37
17
A
VAL
70
-116.24
-79.29
17
A
LEU
71
-144.21
40.03
17
A
LEU
99
-91.56
-60.55
17
A
LEU
120
-91.87
38.50
18
A
LYS
36
133.57
-179.36
18
A
LYS
49
-52.42
-72.15
18
A
PRO
61
-77.89
47.88
18
A
VAL
70
-99.92
-78.87
18
A
ASN
101
-95.97
44.31
18
A
LEU
120
-92.20
38.89
19
A
ASP
18
-140.13
28.47
19
A
LYS
36
139.51
178.53
19
A
LYS
49
-55.02
-72.73
19
A
PRO
61
-87.52
37.80
19
A
VAL
70
-86.98
-79.07
19
A
LEU
71
-146.85
50.26
19
A
ARG
103
-111.06
-77.31
19
A
LEU
120
-90.77
37.47
20
A
ARG
14
-68.75
98.11
20
A
LYS
36
166.66
-178.75
20
A
LYS
49
-53.12
-72.03
20
A
GLU
66
-77.51
-169.37
20
A
VAL
70
-75.07
-79.01
20
A
LEU
120
-90.93
36.63
20
A
SER
121
57.75
-166.91
SOLUTION STRUCTURE OF THE VAM7P PX DOMAIN
1
N
N
A
ARG
41
A
ARG
34
HELX_P
A
GLY
57
A
GLY
50
1
1
17
A
ASP
81
A
ASP
74
HELX_P
A
ASN
101
A
ASN
94
1
2
21
A
SER
106
A
SER
99
HELX_P
A
THR
111
A
THR
104
1
3
6
A
THR
111
A
THR
104
HELX_P
A
LEU
118
A
LEU
111
1
4
8
ENDOCYTOSIS/EXOCYTOSIS
PX domain, Vam7p, phosphoinositide binding, ENDOCYTOSIS-EXOCYTOSIS COMPLEX
VAM7_YEAST
UNP
1
1
P32912
MAANSVGKMSEKLRIKVDDVKINPKYVLYGVSTPNKRLYKRYSEFWKLKTRLERDVGSTIPYDFPEKPGVLDRRWQRRYD
DPEMIDERRIGLERFLNELYNDRFDSRWRDTKIAQDFLQLSKPNVSQEKSQQHLETADEVGWDEMIRDIKLDLDKESDGT
PSVRGALRARTKLHKLRERLEQDVQKKSLPSTEVTRRAALLRSLLKECDDIGTANIAQDRGRLLGVATSDNSSTTEVQGR
TNNDLQQGQMQMVRDQEQELVALHRIIQAQRGLALEMNEELQTQNELLTALEDDVDNTGRRLQIANKKARHFNNSA
8
124
1KMD
8
124
P32912
A
1
1
117
3
3
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LEU
38
A
LEU
31
A
LYS
40
A
LYS
33
A
VAL
27
A
VAL
20
A
SER
32
A
SER
25
A
LYS
16
A
LYS
9
A
VAL
17
A
VAL
10
A
LEU
38
A
LEU
31
A
LYS
40
A
LYS
33
A
VAL
27
A
VAL
20
A
SER
32
A
SER
25
A
LYS
21
A
LYS
14
A
ILE
22
A
ILE
15