1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Dong, G.
Hoffman, D.W.
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 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
UK
EMBO J.
EMJODG
0897
0261-4189
21
1845
1854
10.1093/emboj/21.7.1845
11927568
Structure of small protein B: the protein component of the tmRNA-SmpB system for ribosome rescue.
2002
10.2210/pdb1k8h/pdb
pdb_00001k8h
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
15523.292
Small protein B
1
man
polymer
SSRA-BINDING PROTEIN
no
no
GKSDKIIPIAENKEAKAKYDILETYEAGIVLKGSEVKSLREKGTVSFKDSFVRIENGEAWLYNLYIAPYKHATIENHDPL
RKRKLLLHKREIMRLYGKVQEKGYTIIPLKLYWKNNKVKVLIALAKGKKLYDR
GKSDKIIPIAENKEAKAKYDILETYEAGIVLKGSEVKSLREKGTVSFKDSFVRIENGEAWLYNLYIAPYKHATIENHDPL
RKRKLLLHKREIMRLYGKVQEKGYTIIPLKLYWKNNKVKVLIALAKGKKLYDR
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Aquifex
Escherichia
sample
63363
Aquifex aeolicus
562
Escherichia coli
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2002-03-20
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
2001-10-24
REL
REL
This structure was solved using standard 2D and 3D heteronuclear NMR techniques.
structures with the lowest energy
200
10
2D_NOESY
3D_13C-separated_NOESY
3D_15N-separated_NOESY
100 mM
6.0
ambient
303
K
simulated annealing
1
closest to the average
1 mM SmpB
90% H2O/10% D2O
Brunger
refinement
CNS
1.0
500
Varian
INOVA
GLY
1
n
1
GLY
1
A
LYS
2
n
2
LYS
2
A
SER
3
n
3
SER
3
A
ASP
4
n
4
ASP
4
A
LYS
5
n
5
LYS
5
A
ILE
6
n
6
ILE
6
A
ILE
7
n
7
ILE
7
A
PRO
8
n
8
PRO
8
A
ILE
9
n
9
ILE
9
A
ALA
10
n
10
ALA
10
A
GLU
11
n
11
GLU
11
A
ASN
12
n
12
ASN
12
A
LYS
13
n
13
LYS
13
A
GLU
14
n
14
GLU
14
A
ALA
15
n
15
ALA
15
A
LYS
16
n
16
LYS
16
A
ALA
17
n
17
ALA
17
A
LYS
18
n
18
LYS
18
A
TYR
19
n
19
TYR
19
A
ASP
20
n
20
ASP
20
A
ILE
21
n
21
ILE
21
A
LEU
22
n
22
LEU
22
A
GLU
23
n
23
GLU
23
A
THR
24
n
24
THR
24
A
TYR
25
n
25
TYR
25
A
GLU
26
n
26
GLU
26
A
ALA
27
n
27
ALA
27
A
GLY
28
n
28
GLY
28
A
ILE
29
n
29
ILE
29
A
VAL
30
n
30
VAL
30
A
LEU
31
n
31
LEU
31
A
LYS
32
n
32
LYS
32
A
GLY
33
n
33
GLY
33
A
SER
34
n
34
SER
34
A
GLU
35
n
35
GLU
35
A
VAL
36
n
36
VAL
36
A
LYS
37
n
37
LYS
37
A
SER
38
n
38
SER
38
A
LEU
39
n
39
LEU
39
A
ARG
40
n
40
ARG
40
A
GLU
41
n
41
GLU
41
A
LYS
42
n
42
LYS
42
A
GLY
43
n
43
GLY
43
A
THR
44
n
44
THR
44
A
VAL
45
n
45
VAL
45
A
SER
46
n
46
SER
46
A
PHE
47
n
47
PHE
47
A
LYS
48
n
48
LYS
48
A
ASP
49
n
49
ASP
49
A
SER
50
n
50
SER
50
A
PHE
51
n
51
PHE
51
A
VAL
52
n
52
VAL
52
A
ARG
53
n
53
ARG
53
A
ILE
54
n
54
ILE
54
A
GLU
55
n
55
GLU
55
A
ASN
56
n
56
ASN
56
A
GLY
57
n
57
GLY
57
A
GLU
58
n
58
GLU
58
A
ALA
59
n
59
ALA
59
A
TRP
60
n
60
TRP
60
A
LEU
61
n
61
LEU
61
A
TYR
62
n
62
TYR
62
A
ASN
63
n
63
ASN
63
A
LEU
64
n
64
LEU
64
A
TYR
65
n
65
TYR
65
A
ILE
66
n
66
ILE
66
A
ALA
67
n
67
ALA
67
A
PRO
68
n
68
PRO
68
A
TYR
69
n
69
TYR
69
A
LYS
70
n
70
LYS
70
A
HIS
71
n
71
HIS
71
A
ALA
72
n
72
ALA
72
A
THR
73
n
73
THR
73
A
ILE
74
n
74
ILE
74
A
GLU
75
n
75
GLU
75
A
ASN
76
n
76
ASN
76
A
HIS
77
n
77
HIS
77
A
ASP
78
n
78
ASP
78
A
PRO
79
n
79
PRO
79
A
LEU
80
n
80
LEU
80
A
ARG
81
n
81
ARG
81
A
LYS
82
n
82
LYS
82
A
ARG
83
n
83
ARG
83
A
LYS
84
n
84
LYS
84
A
LEU
85
n
85
LEU
85
A
LEU
86
n
86
LEU
86
A
LEU
87
n
87
LEU
87
A
HIS
88
n
88
HIS
88
A
LYS
89
n
89
LYS
89
A
ARG
90
n
90
ARG
90
A
GLU
91
n
91
GLU
91
A
ILE
92
n
92
ILE
92
A
MET
93
n
93
MET
93
A
ARG
94
n
94
ARG
94
A
LEU
95
n
95
LEU
95
A
TYR
96
n
96
TYR
96
A
GLY
97
n
97
GLY
97
A
LYS
98
n
98
LYS
98
A
VAL
99
n
99
VAL
99
A
GLN
100
n
100
GLN
100
A
GLU
101
n
101
GLU
101
A
LYS
102
n
102
LYS
102
A
GLY
103
n
103
GLY
103
A
TYR
104
n
104
TYR
104
A
THR
105
n
105
THR
105
A
ILE
106
n
106
ILE
106
A
ILE
107
n
107
ILE
107
A
PRO
108
n
108
PRO
108
A
LEU
109
n
109
LEU
109
A
LYS
110
n
110
LYS
110
A
LEU
111
n
111
LEU
111
A
TYR
112
n
112
TYR
112
A
TRP
113
n
113
TRP
113
A
LYS
114
n
114
LYS
114
A
ASN
115
n
115
ASN
115
A
ASN
116
n
116
ASN
116
A
LYS
117
n
117
LYS
117
A
VAL
118
n
118
VAL
118
A
LYS
119
n
119
LYS
119
A
VAL
120
n
120
VAL
120
A
LEU
121
n
121
LEU
121
A
ILE
122
n
122
ILE
122
A
ALA
123
n
123
ALA
123
A
LEU
124
n
124
LEU
124
A
ALA
125
n
125
ALA
125
A
LYS
126
n
126
LYS
126
A
GLY
127
n
127
GLY
127
A
LYS
128
n
128
LYS
128
A
LYS
129
n
129
LYS
129
A
LEU
130
n
130
LEU
130
A
TYR
131
n
131
TYR
131
A
ASP
132
n
132
ASP
132
A
ARG
133
n
133
ARG
133
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
ALA
27
A
N
ALA
27
A
O
VAL
120
A
O
VAL
120
A
O
LYS
119
A
O
LYS
119
A
N
TYR
112
A
N
TYR
112
A
N
PHE
51
A
N
PHE
51
A
O
TYR
62
A
O
TYR
62
A
N
LEU
61
A
N
LEU
61
A
O
ARG
83
A
O
ARG
83
1
A
LYS
2
-98.93
-60.06
1
A
SER
3
-75.48
-169.56
1
A
ASP
4
60.58
179.64
1
A
LYS
5
-148.53
27.63
1
A
ALA
10
54.06
168.09
1
A
LYS
13
174.49
-34.23
1
A
LEU
22
-109.95
-68.77
1
A
LYS
32
-57.07
-166.36
1
A
LYS
42
-57.44
-82.15
1
A
PHE
47
-120.87
-68.91
1
A
ASN
56
54.58
-96.07
1
A
TYR
65
-148.07
46.81
1
A
PRO
68
-47.93
160.58
1
A
ILE
74
-98.82
33.34
1
A
LEU
80
-130.54
-51.02
1
A
ARG
81
54.29
79.75
1
A
LEU
86
-49.27
174.19
1
A
LEU
87
-172.68
-156.26
1
A
HIS
88
-105.33
-160.65
1
A
LEU
109
-123.75
-99.70
1
A
ASN
115
73.45
-57.46
1
A
ASN
116
-177.22
-7.44
1
A
LYS
128
61.78
155.79
1
A
LYS
129
-175.73
-175.48
1
A
LEU
130
63.79
-79.37
2
A
ASP
4
57.11
104.74
2
A
ALA
10
55.23
164.68
2
A
GLU
11
179.53
102.11
2
A
LYS
13
-162.69
33.73
2
A
LYS
18
-156.63
77.12
2
A
TYR
19
175.96
122.60
2
A
LEU
22
-130.07
-69.33
2
A
LYS
32
-164.39
69.31
2
A
SER
34
82.86
-41.45
2
A
LYS
42
-165.24
78.47
2
A
VAL
45
51.63
161.56
2
A
PHE
47
-170.67
121.92
2
A
LYS
48
60.11
-179.64
2
A
ASP
49
80.12
-13.05
2
A
ASN
56
55.68
-102.83
2
A
LYS
70
-172.52
99.67
2
A
GLU
75
63.11
127.17
2
A
HIS
77
68.81
-67.66
2
A
LEU
87
-138.47
-130.24
2
A
HIS
88
-125.40
-84.17
2
A
LYS
89
174.09
-72.68
2
A
VAL
99
-49.90
-70.24
2
A
LEU
109
-123.04
-98.89
2
A
ASN
115
72.32
-56.27
2
A
ASN
116
-177.58
-11.78
2
A
LYS
128
177.81
-49.37
2
A
LYS
129
-178.10
79.92
3
A
LYS
2
60.39
163.15
3
A
ASP
4
-148.45
41.26
3
A
ALA
10
55.75
160.28
3
A
GLU
11
-178.28
133.63
3
A
ASN
12
-177.28
135.93
3
A
LYS
18
-134.80
-78.19
3
A
TYR
19
-41.18
104.21
3
A
LEU
22
-102.77
-82.94
3
A
LEU
31
60.93
172.72
3
A
LYS
32
-143.74
16.50
3
A
LYS
42
-176.55
76.87
3
A
THR
44
-162.61
119.15
3
A
PHE
47
-164.58
-169.01
3
A
ASN
56
59.86
-88.63
3
A
TYR
69
-163.32
31.06
3
A
GLU
75
61.57
178.24
3
A
ASP
78
62.26
116.36
3
A
PRO
79
-65.44
63.29
3
A
LEU
80
-149.95
-73.36
3
A
ARG
81
50.23
-177.59
3
A
LEU
86
-68.45
-178.11
3
A
LEU
87
-166.41
-156.73
3
A
HIS
88
-96.78
-83.71
3
A
LYS
89
173.13
-62.73
3
A
LEU
109
-125.38
-100.77
3
A
ASN
115
73.09
-55.56
3
A
ASN
116
-178.09
-9.34
3
A
LYS
129
-146.38
-58.74
3
A
LEU
130
63.02
123.48
3
A
ASP
132
60.96
157.89
4
A
ALA
10
51.37
175.13
4
A
LYS
13
175.81
-37.46
4
A
LEU
22
-132.02
-78.60
4
A
LEU
31
-174.82
-176.66
4
A
LYS
32
-176.88
136.44
4
A
SER
34
177.43
-31.01
4
A
LYS
42
-51.80
-79.49
4
A
SER
46
73.50
-164.36
4
A
PHE
47
67.69
107.02
4
A
LYS
48
62.32
151.22
4
A
ASN
56
-41.33
92.29
4
A
TYR
69
-128.58
-50.46
4
A
HIS
71
-98.80
33.33
4
A
ASN
76
59.85
-177.35
4
A
LEU
80
-132.10
-50.44
4
A
ARG
81
60.92
-179.81
4
A
LEU
109
-109.88
-99.10
4
A
ASN
115
73.61
-54.24
4
A
ASN
116
-179.87
-9.14
4
A
LYS
128
61.67
152.56
4
A
LYS
129
43.57
-165.76
4
A
TYR
131
-154.58
-46.43
5
A
SER
3
61.19
155.82
5
A
ALA
10
61.44
-82.05
5
A
GLU
11
47.05
96.11
5
A
LYS
13
-147.20
36.84
5
A
TYR
19
174.87
119.22
5
A
LEU
22
-135.79
-69.35
5
A
LYS
42
-177.53
79.04
5
A
PHE
47
-178.77
79.38
5
A
ASP
49
-176.92
80.52
5
A
ASN
56
53.15
-91.29
5
A
LEU
64
-168.28
48.36
5
A
PRO
68
-58.14
-160.50
5
A
HIS
71
63.29
98.64
5
A
ALA
72
-144.34
-77.31
5
A
THR
73
-178.07
-39.98
5
A
GLU
75
58.79
167.33
5
A
HIS
77
54.96
175.20
5
A
PRO
79
-55.64
-70.24
5
A
HIS
88
-64.59
-170.08
5
A
LEU
109
-123.07
-97.91
5
A
ASN
115
73.24
-54.28
5
A
ASN
116
-178.98
-10.63
5
A
LYS
128
62.69
-169.54
5
A
ASP
132
59.86
101.75
6
A
ALA
10
68.41
-84.59
6
A
GLU
11
55.49
107.80
6
A
ASN
12
-171.89
110.44
6
A
LEU
22
-133.47
-45.96
6
A
SER
34
174.55
-41.31
6
A
LYS
42
175.90
77.85
6
A
SER
46
179.60
146.32
6
A
PHE
47
-158.66
44.12
6
A
ASP
49
-147.41
15.18
6
A
ASN
56
54.64
-91.10
6
A
TYR
65
-170.32
92.46
6
A
PRO
68
-52.94
173.20
6
A
ILE
74
-151.88
72.24
6
A
ASP
78
-160.41
-65.76
6
A
ARG
81
-108.27
-166.70
6
A
LEU
87
-179.65
-149.91
6
A
VAL
99
-52.11
-70.60
6
A
LEU
109
-113.04
-90.89
6
A
ASN
115
72.59
-58.84
6
A
ASN
116
-177.03
-5.49
7
A
LYS
5
-162.87
89.98
7
A
ALA
10
55.08
157.93
7
A
GLU
11
178.82
108.56
7
A
LYS
13
-156.80
28.73
7
A
LYS
18
-124.08
-72.22
7
A
TYR
19
-56.37
104.93
7
A
LEU
22
-128.52
-70.38
7
A
LYS
42
-67.29
-81.51
7
A
THR
44
-106.81
-157.15
7
A
VAL
45
59.04
142.88
7
A
SER
46
59.33
83.52
7
A
PHE
47
-135.87
-58.22
7
A
LYS
48
-160.06
29.33
7
A
ASP
49
-155.01
26.48
7
A
ASN
56
-34.98
93.03
7
A
TYR
65
-90.75
50.26
7
A
ILE
66
-101.44
-165.51
7
A
ALA
67
76.93
89.99
7
A
TYR
69
62.21
134.04
7
A
LYS
70
-176.51
58.74
7
A
HIS
71
59.70
168.07
7
A
ALA
72
63.46
132.16
7
A
THR
73
60.48
102.80
7
A
ASN
76
63.78
-80.69
7
A
HIS
77
56.03
71.10
7
A
PRO
79
-81.58
49.99
7
A
LEU
80
177.22
128.48
7
A
LEU
87
-141.41
-154.72
7
A
HIS
88
-103.56
-90.29
7
A
LYS
89
-168.09
-70.00
7
A
LEU
109
-99.82
-89.83
7
A
ASN
115
73.02
-53.98
7
A
ASN
116
179.86
-9.65
7
A
LYS
128
61.77
175.65
7
A
TYR
131
60.36
163.08
8
A
ALA
10
54.99
157.25
8
A
GLU
11
-178.27
127.77
8
A
ASN
12
179.32
134.85
8
A
LYS
18
-117.11
-80.19
8
A
TYR
19
-48.15
107.64
8
A
LEU
22
-129.23
-69.56
8
A
LYS
32
-149.71
-57.76
8
A
LYS
42
-176.58
73.96
8
A
SER
46
-73.67
-77.57
8
A
ASP
49
175.48
81.69
8
A
ASN
56
57.36
-95.27
8
A
TYR
69
-177.76
108.47
8
A
HIS
71
-155.57
25.83
8
A
ALA
72
52.59
-177.16
8
A
THR
73
57.42
81.70
8
A
ASN
76
61.05
65.46
8
A
LEU
87
-179.09
146.14
8
A
HIS
88
-63.11
-176.01
8
A
VAL
99
-53.52
-70.53
8
A
LEU
109
-122.64
-97.26
8
A
ASN
115
72.78
-56.97
8
A
ASN
116
-177.43
-11.24
8
A
TYR
131
-168.91
-60.44
9
A
SER
3
60.65
107.54
9
A
ALA
10
52.65
159.04
9
A
GLU
11
179.71
141.14
9
A
LYS
13
-157.33
17.54
9
A
LEU
22
-138.23
-63.53
9
A
LEU
31
-49.80
178.18
9
A
LYS
42
-173.16
80.54
9
A
PHE
47
58.89
-170.26
9
A
ASP
49
-175.15
38.13
9
A
ASN
56
-37.47
95.64
9
A
TYR
65
178.82
69.98
9
A
TYR
69
62.55
148.55
9
A
LYS
70
-95.53
-70.24
9
A
HIS
71
-69.30
-176.45
9
A
THR
73
-150.54
-153.99
9
A
ILE
74
-91.73
31.60
9
A
GLU
75
57.89
97.94
9
A
ASN
76
-164.12
31.76
9
A
HIS
88
-93.32
-74.46
9
A
LYS
89
167.79
-76.36
9
A
VAL
99
-49.79
-70.88
9
A
LEU
109
-120.65
-93.64
9
A
ASN
115
73.39
-55.76
9
A
ASN
116
-178.56
-8.25
9
A
LYS
128
61.53
155.03
9
A
TYR
131
-131.30
-46.65
10
A
LYS
2
60.65
104.99
10
A
ASP
4
-125.28
-76.50
10
A
LYS
5
-163.03
30.64
10
A
ALA
10
69.86
156.16
10
A
LYS
13
-177.12
38.23
10
A
LYS
18
-125.99
-69.11
10
A
TYR
19
-42.65
105.53
10
A
LEU
22
-130.11
-65.94
10
A
LEU
31
-54.92
-176.70
10
A
LYS
32
-142.96
-81.78
10
A
LYS
42
-165.16
82.61
10
A
THR
44
-90.37
-147.00
10
A
VAL
45
45.68
95.34
10
A
PHE
47
-72.78
-164.88
10
A
LYS
48
-115.16
62.28
10
A
ASN
56
-33.19
94.02
10
A
PRO
68
-70.36
-167.87
10
A
HIS
71
-137.95
-48.64
10
A
ASP
78
-158.14
64.61
10
A
VAL
99
-49.71
-70.33
10
A
LEU
109
-117.56
-101.51
10
A
ASN
115
73.03
-54.52
10
A
ASN
116
-179.65
-12.26
10
A
LYS
128
60.72
103.33
10
A
LYS
129
-59.13
96.00
10
A
ASP
132
59.84
73.44
NMR Structure of Small Protein B (SmpB) from Aquifex aeolicus
1
N
N
A
LYS
13
A
LYS
13
HELX_P
A
TYR
19
A
TYR
19
1
1
7
A
GLY
33
A
GLY
33
HELX_P
A
GLY
43
A
GLY
43
1
2
11
A
LYS
89
A
LYS
89
HELX_P
A
GLY
103
A
GLY
103
1
3
15
RNA BINDING PROTEIN
SmpB, SsrA associated protein, RNA BINDING PROTEIN
SSRP_AQUAE
UNP
1
2
O66640
GKSDKIIPIAENKEAKAKYDILETYEAGIVLKGSEVKSLREKGTVSFKDSFVRIENGEAWLYNLYIAPYKHATIENHDPL
RKRKLLLHKREIMRLYGKVQEKGYTIIPLKLYWKNNKVKVLIALAKGKKLYDR
2
134
1K8H
1
133
O66640
A
1
1
133
3
3
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ILE
21
A
ILE
21
A
ILE
29
A
ILE
29
A
LYS
117
A
LYS
117
A
ALA
125
A
ALA
125
A
THR
105
A
THR
105
A
LYS
114
A
LYS
114
A
SER
50
A
SER
50
A
GLU
55
A
GLU
55
A
GLU
58
A
GLU
58
A
ASN
63
A
ASN
63
A
ARG
83
A
ARG
83
A
LEU
85
A
LEU
85