0.013941
0.008049
0.000000
0.000000
0.016098
0.000000
0.000000
0.000000
0.006501
0.00000
0.00000
0.00000
Gallois-montbrun, S.
Chen, Y.
Dutartre, H.
Morera, S.
Guerreiro, C.
Mulard, L.
Schneider, B.
Janin, J.
Canard, B.
Veron, M.
Deville-bonne, D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
18
90.00
90.00
120.00
71.731
71.731
153.818
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
H2 O
18.015
WATER
non-polymer
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
Mg 2
24.305
MAGNESIUM ION
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C8 H15 N4 O14 P3
484.144
RIBAVIRIN TRIPHOSPHATE
RNA 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
MOL.PHARMACOL.
MOPMA3
0197
0026-895X
63
538
546
10.1124/mol.63.3.538
12606760
Structural Analysis of the Activation of Ribavirin Analogs by NDP Kinase: Comparison with Other Ribavirin Targets
2003
10.2210/pdb1mn9/pdb
pdb_00001mn9
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
IMAGE PLATE
2001-06-10
MARRESEARCH
GRAPHITE
SINGLE WAVELENGTH
M
x-ray
1
1.542
1.0
1.542
ROTATING ANODE
RIGAKU RU300
16735.242
NDP kinase
2.7.4.6
H122G
3
man
polymer
24.305
MAGNESIUM ION
3
syn
non-polymer
484.144
RIBAVIRIN TRIPHOSPHATE
3
syn
non-polymer
18.015
water
38
nat
water
Nucleoside diphosphate kinase, cytosolic
no
no
MSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAM
VFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE
MSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAM
VFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE
A,B,C
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Dictyostelium
Escherichia
sample
44689
Dictyostelium discoideum
562
Escherichia coli
1
2.27
45.91
VAPOR DIFFUSION, HANGING DROP
7.5
PEG 550, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
database_2
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Derived calculations
Version format compliance
Database references
Derived calculations
1
0
2003-03-18
1
1
2008-04-28
1
2
2011-07-13
1
3
2021-11-10
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr2_auth_asym_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
1F3F contains the same protein complexed with D4T-Triphosphate and Mg
1NUE contains human nucleoside diphosphate kinase B complexed with GDP
RCSB
Y
PDBJ
2002-09-05
REL
REL
MG
MAGNESIUM ION
RTP
RIBAVIRIN TRIPHOSPHATE
HOH
water
MG2
164
2
MG
MG
164
A
RTP
160
3
RTP
RTP
160
A
RTP
161
3
RTP
RTP
161
A
RTP
162
3
RTP
RTP
162
A
MG2
163
2
MG
MG
163
B
MG2
165
2
MG
MG
165
C
HOH
1001
4
HOH
HOH
1001
A
HOH
1002
4
HOH
HOH
1002
A
HOH
1003
4
HOH
HOH
1003
A
HOH
1004
4
HOH
HOH
1004
A
HOH
1005
4
HOH
HOH
1005
A
HOH
1016
4
HOH
HOH
1016
A
HOH
1020
4
HOH
HOH
1020
A
HOH
1021
4
HOH
HOH
1021
A
HOH
1023
4
HOH
HOH
1023
A
HOH
1032
4
HOH
HOH
1032
A
HOH
1033
4
HOH
HOH
1033
A
HOH
1036
4
HOH
HOH
1036
A
HOH
1037
4
HOH
HOH
1037
A
HOH
1006
4
HOH
HOH
1006
B
HOH
1007
4
HOH
HOH
1007
B
HOH
1008
4
HOH
HOH
1008
B
HOH
1009
4
HOH
HOH
1009
B
HOH
1013
4
HOH
HOH
1013
B
HOH
1014
4
HOH
HOH
1014
B
HOH
1015
4
HOH
HOH
1015
B
HOH
1017
4
HOH
HOH
1017
B
HOH
1018
4
HOH
HOH
1018
B
HOH
1019
4
HOH
HOH
1019
B
HOH
1022
4
HOH
HOH
1022
B
HOH
1025
4
HOH
HOH
1025
B
HOH
1026
4
HOH
HOH
1026
B
HOH
1028
4
HOH
HOH
1028
B
HOH
1031
4
HOH
HOH
1031
B
HOH
1034
4
HOH
HOH
1034
B
HOH
1035
4
HOH
HOH
1035
B
HOH
1010
4
HOH
HOH
1010
C
HOH
1011
4
HOH
HOH
1011
C
HOH
1012
4
HOH
HOH
1012
C
HOH
1024
4
HOH
HOH
1024
C
HOH
1027
4
HOH
HOH
1027
C
HOH
1029
4
HOH
HOH
1029
C
HOH
1030
4
HOH
HOH
1030
C
HOH
1038
4
HOH
HOH
1038
C
n
1
1
A
n
2
2
A
n
3
3
A
n
4
4
A
n
5
5
A
VAL
6
n
6
VAL
6
A
ASN
7
n
7
ASN
7
A
LYS
8
n
8
LYS
8
A
GLU
9
n
9
GLU
9
A
ARG
10
n
10
ARG
10
A
THR
11
n
11
THR
11
A
PHE
12
n
12
PHE
12
A
LEU
13
n
13
LEU
13
A
ALA
14
n
14
ALA
14
A
VAL
15
n
15
VAL
15
A
LYS
16
n
16
LYS
16
A
PRO
17
n
17
PRO
17
A
ASP
18
n
18
ASP
18
A
GLY
19
n
19
GLY
19
A
VAL
20
n
20
VAL
20
A
ALA
21
n
21
ALA
21
A
ARG
22
n
22
ARG
22
A
GLY
23
n
23
GLY
23
A
LEU
24
n
24
LEU
24
A
VAL
25
n
25
VAL
25
A
GLY
26
n
26
GLY
26
A
GLU
27
n
27
GLU
27
A
ILE
28
n
28
ILE
28
A
ILE
29
n
29
ILE
29
A
ALA
30
n
30
ALA
30
A
ARG
31
n
31
ARG
31
A
TYR
32
n
32
TYR
32
A
GLU
33
n
33
GLU
33
A
LYS
34
n
34
LYS
34
A
LYS
35
n
35
LYS
35
A
GLY
36
n
36
GLY
36
A
PHE
37
n
37
PHE
37
A
VAL
38
n
38
VAL
38
A
LEU
39
n
39
LEU
39
A
VAL
40
n
40
VAL
40
A
GLY
41
n
41
GLY
41
A
LEU
42
n
42
LEU
42
A
LYS
43
n
43
LYS
43
A
GLN
44
n
44
GLN
44
A
LEU
45
n
45
LEU
45
A
VAL
46
n
46
VAL
46
A
PRO
47
n
47
PRO
47
A
THR
48
n
48
THR
48
A
LYS
49
n
49
LYS
49
A
ASP
50
n
50
ASP
50
A
LEU
51
n
51
LEU
51
A
ALA
52
n
52
ALA
52
A
GLU
53
n
53
GLU
53
A
SER
54
n
54
SER
54
A
HIS
55
n
55
HIS
55
A
TYR
56
n
56
TYR
56
A
ALA
57
n
57
ALA
57
A
GLU
58
n
58
GLU
58
A
HIS
59
n
59
HIS
59
A
LYS
60
n
60
LYS
60
A
GLU
61
n
61
GLU
61
A
ARG
62
n
62
ARG
62
A
PRO
63
n
63
PRO
63
A
PHE
64
n
64
PHE
64
A
PHE
65
n
65
PHE
65
A
GLY
66
n
66
GLY
66
A
GLY
67
n
67
GLY
67
A
LEU
68
n
68
LEU
68
A
VAL
69
n
69
VAL
69
A
SER
70
n
70
SER
70
A
PHE
71
n
71
PHE
71
A
ILE
72
n
72
ILE
72
A
THR
73
n
73
THR
73
A
SER
74
n
74
SER
74
A
GLY
75
n
75
GLY
75
A
PRO
76
n
76
PRO
76
A
VAL
77
n
77
VAL
77
A
VAL
78
n
78
VAL
78
A
ALA
79
n
79
ALA
79
A
MET
80
n
80
MET
80
A
VAL
81
n
81
VAL
81
A
PHE
82
n
82
PHE
82
A
GLU
83
n
83
GLU
83
A
GLY
84
n
84
GLY
84
A
LYS
85
n
85
LYS
85
A
GLY
86
n
86
GLY
86
A
VAL
87
n
87
VAL
87
A
VAL
88
n
88
VAL
88
A
ALA
89
n
89
ALA
89
A
SER
90
n
90
SER
90
A
ALA
91
n
91
ALA
91
A
ARG
92
n
92
ARG
92
A
LEU
93
n
93
LEU
93
A
MET
94
n
94
MET
94
A
ILE
95
n
95
ILE
95
A
GLY
96
n
96
GLY
96
A
VAL
97
n
97
VAL
97
A
THR
98
n
98
THR
98
A
ASN
99
n
99
ASN
99
A
PRO
100
n
100
PRO
100
A
LEU
101
n
101
LEU
101
A
ALA
102
n
102
ALA
102
A
SER
103
n
103
SER
103
A
ALA
104
n
104
ALA
104
A
PRO
105
n
105
PRO
105
A
GLY
106
n
106
GLY
106
A
SER
107
n
107
SER
107
A
ILE
108
n
108
ILE
108
A
ARG
109
n
109
ARG
109
A
GLY
110
n
110
GLY
110
A
ASP
111
n
111
ASP
111
A
PHE
112
n
112
PHE
112
A
GLY
113
n
113
GLY
113
A
VAL
114
n
114
VAL
114
A
ASP
115
n
115
ASP
115
A
VAL
116
n
116
VAL
116
A
GLY
117
n
117
GLY
117
A
ARG
118
n
118
ARG
118
A
ASN
119
n
119
ASN
119
A
ILE
120
n
120
ILE
120
A
ILE
121
n
121
ILE
121
A
GLY
122
n
122
GLY
122
A
GLY
123
n
123
GLY
123
A
SER
124
n
124
SER
124
A
ASP
125
n
125
ASP
125
A
SER
126
n
126
SER
126
A
VAL
127
n
127
VAL
127
A
GLU
128
n
128
GLU
128
A
SER
129
n
129
SER
129
A
ALA
130
n
130
ALA
130
A
ASN
131
n
131
ASN
131
A
ARG
132
n
132
ARG
132
A
GLU
133
n
133
GLU
133
A
ILE
134
n
134
ILE
134
A
ALA
135
n
135
ALA
135
A
LEU
136
n
136
LEU
136
A
TRP
137
n
137
TRP
137
A
PHE
138
n
138
PHE
138
A
LYS
139
n
139
LYS
139
A
PRO
140
n
140
PRO
140
A
GLU
141
n
141
GLU
141
A
GLU
142
n
142
GLU
142
A
LEU
143
n
143
LEU
143
A
LEU
144
n
144
LEU
144
A
THR
145
n
145
THR
145
A
GLU
146
n
146
GLU
146
A
VAL
147
n
147
VAL
147
A
LYS
148
n
148
LYS
148
A
PRO
149
n
149
PRO
149
A
ASN
150
n
150
ASN
150
A
PRO
151
n
151
PRO
151
A
ASN
152
n
152
ASN
152
A
LEU
153
n
153
LEU
153
A
TYR
154
n
154
TYR
154
A
GLU
155
n
155
GLU
155
A
n
1
1
B
n
2
2
B
n
3
3
B
n
4
4
B
n
5
5
B
VAL
6
n
6
VAL
6
B
ASN
7
n
7
ASN
7
B
LYS
8
n
8
LYS
8
B
GLU
9
n
9
GLU
9
B
ARG
10
n
10
ARG
10
B
THR
11
n
11
THR
11
B
PHE
12
n
12
PHE
12
B
LEU
13
n
13
LEU
13
B
ALA
14
n
14
ALA
14
B
VAL
15
n
15
VAL
15
B
LYS
16
n
16
LYS
16
B
PRO
17
n
17
PRO
17
B
ASP
18
n
18
ASP
18
B
GLY
19
n
19
GLY
19
B
VAL
20
n
20
VAL
20
B
ALA
21
n
21
ALA
21
B
ARG
22
n
22
ARG
22
B
GLY
23
n
23
GLY
23
B
LEU
24
n
24
LEU
24
B
VAL
25
n
25
VAL
25
B
GLY
26
n
26
GLY
26
B
GLU
27
n
27
GLU
27
B
ILE
28
n
28
ILE
28
B
ILE
29
n
29
ILE
29
B
ALA
30
n
30
ALA
30
B
ARG
31
n
31
ARG
31
B
TYR
32
n
32
TYR
32
B
GLU
33
n
33
GLU
33
B
LYS
34
n
34
LYS
34
B
LYS
35
n
35
LYS
35
B
GLY
36
n
36
GLY
36
B
PHE
37
n
37
PHE
37
B
VAL
38
n
38
VAL
38
B
LEU
39
n
39
LEU
39
B
VAL
40
n
40
VAL
40
B
GLY
41
n
41
GLY
41
B
LEU
42
n
42
LEU
42
B
LYS
43
n
43
LYS
43
B
GLN
44
n
44
GLN
44
B
LEU
45
n
45
LEU
45
B
VAL
46
n
46
VAL
46
B
PRO
47
n
47
PRO
47
B
THR
48
n
48
THR
48
B
LYS
49
n
49
LYS
49
B
ASP
50
n
50
ASP
50
B
LEU
51
n
51
LEU
51
B
ALA
52
n
52
ALA
52
B
GLU
53
n
53
GLU
53
B
SER
54
n
54
SER
54
B
HIS
55
n
55
HIS
55
B
TYR
56
n
56
TYR
56
B
ALA
57
n
57
ALA
57
B
GLU
58
n
58
GLU
58
B
HIS
59
n
59
HIS
59
B
LYS
60
n
60
LYS
60
B
GLU
61
n
61
GLU
61
B
ARG
62
n
62
ARG
62
B
PRO
63
n
63
PRO
63
B
PHE
64
n
64
PHE
64
B
PHE
65
n
65
PHE
65
B
GLY
66
n
66
GLY
66
B
GLY
67
n
67
GLY
67
B
LEU
68
n
68
LEU
68
B
VAL
69
n
69
VAL
69
B
SER
70
n
70
SER
70
B
PHE
71
n
71
PHE
71
B
ILE
72
n
72
ILE
72
B
THR
73
n
73
THR
73
B
SER
74
n
74
SER
74
B
GLY
75
n
75
GLY
75
B
PRO
76
n
76
PRO
76
B
VAL
77
n
77
VAL
77
B
VAL
78
n
78
VAL
78
B
ALA
79
n
79
ALA
79
B
MET
80
n
80
MET
80
B
VAL
81
n
81
VAL
81
B
PHE
82
n
82
PHE
82
B
GLU
83
n
83
GLU
83
B
GLY
84
n
84
GLY
84
B
LYS
85
n
85
LYS
85
B
GLY
86
n
86
GLY
86
B
VAL
87
n
87
VAL
87
B
VAL
88
n
88
VAL
88
B
ALA
89
n
89
ALA
89
B
SER
90
n
90
SER
90
B
ALA
91
n
91
ALA
91
B
ARG
92
n
92
ARG
92
B
LEU
93
n
93
LEU
93
B
MET
94
n
94
MET
94
B
ILE
95
n
95
ILE
95
B
GLY
96
n
96
GLY
96
B
VAL
97
n
97
VAL
97
B
THR
98
n
98
THR
98
B
ASN
99
n
99
ASN
99
B
PRO
100
n
100
PRO
100
B
LEU
101
n
101
LEU
101
B
ALA
102
n
102
ALA
102
B
SER
103
n
103
SER
103
B
ALA
104
n
104
ALA
104
B
PRO
105
n
105
PRO
105
B
GLY
106
n
106
GLY
106
B
SER
107
n
107
SER
107
B
ILE
108
n
108
ILE
108
B
ARG
109
n
109
ARG
109
B
GLY
110
n
110
GLY
110
B
ASP
111
n
111
ASP
111
B
PHE
112
n
112
PHE
112
B
GLY
113
n
113
GLY
113
B
VAL
114
n
114
VAL
114
B
ASP
115
n
115
ASP
115
B
VAL
116
n
116
VAL
116
B
GLY
117
n
117
GLY
117
B
ARG
118
n
118
ARG
118
B
ASN
119
n
119
ASN
119
B
ILE
120
n
120
ILE
120
B
ILE
121
n
121
ILE
121
B
GLY
122
n
122
GLY
122
B
GLY
123
n
123
GLY
123
B
SER
124
n
124
SER
124
B
ASP
125
n
125
ASP
125
B
SER
126
n
126
SER
126
B
VAL
127
n
127
VAL
127
B
GLU
128
n
128
GLU
128
B
SER
129
n
129
SER
129
B
ALA
130
n
130
ALA
130
B
ASN
131
n
131
ASN
131
B
ARG
132
n
132
ARG
132
B
GLU
133
n
133
GLU
133
B
ILE
134
n
134
ILE
134
B
ALA
135
n
135
ALA
135
B
LEU
136
n
136
LEU
136
B
TRP
137
n
137
TRP
137
B
PHE
138
n
138
PHE
138
B
LYS
139
n
139
LYS
139
B
PRO
140
n
140
PRO
140
B
GLU
141
n
141
GLU
141
B
GLU
142
n
142
GLU
142
B
LEU
143
n
143
LEU
143
B
LEU
144
n
144
LEU
144
B
THR
145
n
145
THR
145
B
GLU
146
n
146
GLU
146
B
VAL
147
n
147
VAL
147
B
LYS
148
n
148
LYS
148
B
PRO
149
n
149
PRO
149
B
ASN
150
n
150
ASN
150
B
PRO
151
n
151
PRO
151
B
ASN
152
n
152
ASN
152
B
LEU
153
n
153
LEU
153
B
TYR
154
n
154
TYR
154
B
GLU
155
n
155
GLU
155
B
n
1
1
C
n
2
2
C
n
3
3
C
n
4
4
C
n
5
5
C
VAL
6
n
6
VAL
6
C
ASN
7
n
7
ASN
7
C
LYS
8
n
8
LYS
8
C
GLU
9
n
9
GLU
9
C
ARG
10
n
10
ARG
10
C
THR
11
n
11
THR
11
C
PHE
12
n
12
PHE
12
C
LEU
13
n
13
LEU
13
C
ALA
14
n
14
ALA
14
C
VAL
15
n
15
VAL
15
C
LYS
16
n
16
LYS
16
C
PRO
17
n
17
PRO
17
C
ASP
18
n
18
ASP
18
C
GLY
19
n
19
GLY
19
C
VAL
20
n
20
VAL
20
C
ALA
21
n
21
ALA
21
C
ARG
22
n
22
ARG
22
C
GLY
23
n
23
GLY
23
C
LEU
24
n
24
LEU
24
C
VAL
25
n
25
VAL
25
C
GLY
26
n
26
GLY
26
C
GLU
27
n
27
GLU
27
C
ILE
28
n
28
ILE
28
C
ILE
29
n
29
ILE
29
C
ALA
30
n
30
ALA
30
C
ARG
31
n
31
ARG
31
C
TYR
32
n
32
TYR
32
C
GLU
33
n
33
GLU
33
C
LYS
34
n
34
LYS
34
C
LYS
35
n
35
LYS
35
C
GLY
36
n
36
GLY
36
C
PHE
37
n
37
PHE
37
C
VAL
38
n
38
VAL
38
C
LEU
39
n
39
LEU
39
C
VAL
40
n
40
VAL
40
C
GLY
41
n
41
GLY
41
C
LEU
42
n
42
LEU
42
C
LYS
43
n
43
LYS
43
C
GLN
44
n
44
GLN
44
C
LEU
45
n
45
LEU
45
C
VAL
46
n
46
VAL
46
C
PRO
47
n
47
PRO
47
C
THR
48
n
48
THR
48
C
LYS
49
n
49
LYS
49
C
ASP
50
n
50
ASP
50
C
LEU
51
n
51
LEU
51
C
ALA
52
n
52
ALA
52
C
GLU
53
n
53
GLU
53
C
SER
54
n
54
SER
54
C
HIS
55
n
55
HIS
55
C
TYR
56
n
56
TYR
56
C
ALA
57
n
57
ALA
57
C
GLU
58
n
58
GLU
58
C
HIS
59
n
59
HIS
59
C
LYS
60
n
60
LYS
60
C
GLU
61
n
61
GLU
61
C
ARG
62
n
62
ARG
62
C
PRO
63
n
63
PRO
63
C
PHE
64
n
64
PHE
64
C
PHE
65
n
65
PHE
65
C
GLY
66
n
66
GLY
66
C
GLY
67
n
67
GLY
67
C
LEU
68
n
68
LEU
68
C
VAL
69
n
69
VAL
69
C
SER
70
n
70
SER
70
C
PHE
71
n
71
PHE
71
C
ILE
72
n
72
ILE
72
C
THR
73
n
73
THR
73
C
SER
74
n
74
SER
74
C
GLY
75
n
75
GLY
75
C
PRO
76
n
76
PRO
76
C
VAL
77
n
77
VAL
77
C
VAL
78
n
78
VAL
78
C
ALA
79
n
79
ALA
79
C
MET
80
n
80
MET
80
C
VAL
81
n
81
VAL
81
C
PHE
82
n
82
PHE
82
C
GLU
83
n
83
GLU
83
C
GLY
84
n
84
GLY
84
C
LYS
85
n
85
LYS
85
C
GLY
86
n
86
GLY
86
C
VAL
87
n
87
VAL
87
C
VAL
88
n
88
VAL
88
C
ALA
89
n
89
ALA
89
C
SER
90
n
90
SER
90
C
ALA
91
n
91
ALA
91
C
ARG
92
n
92
ARG
92
C
LEU
93
n
93
LEU
93
C
MET
94
n
94
MET
94
C
ILE
95
n
95
ILE
95
C
GLY
96
n
96
GLY
96
C
VAL
97
n
97
VAL
97
C
THR
98
n
98
THR
98
C
ASN
99
n
99
ASN
99
C
PRO
100
n
100
PRO
100
C
LEU
101
n
101
LEU
101
C
ALA
102
n
102
ALA
102
C
SER
103
n
103
SER
103
C
ALA
104
n
104
ALA
104
C
PRO
105
n
105
PRO
105
C
GLY
106
n
106
GLY
106
C
SER
107
n
107
SER
107
C
ILE
108
n
108
ILE
108
C
ARG
109
n
109
ARG
109
C
GLY
110
n
110
GLY
110
C
ASP
111
n
111
ASP
111
C
PHE
112
n
112
PHE
112
C
GLY
113
n
113
GLY
113
C
VAL
114
n
114
VAL
114
C
ASP
115
n
115
ASP
115
C
VAL
116
n
116
VAL
116
C
GLY
117
n
117
GLY
117
C
ARG
118
n
118
ARG
118
C
ASN
119
n
119
ASN
119
C
ILE
120
n
120
ILE
120
C
ILE
121
n
121
ILE
121
C
GLY
122
n
122
GLY
122
C
GLY
123
n
123
GLY
123
C
SER
124
n
124
SER
124
C
ASP
125
n
125
ASP
125
C
SER
126
n
126
SER
126
C
VAL
127
n
127
VAL
127
C
GLU
128
n
128
GLU
128
C
SER
129
n
129
SER
129
C
ALA
130
n
130
ALA
130
C
ASN
131
n
131
ASN
131
C
ARG
132
n
132
ARG
132
C
GLU
133
n
133
GLU
133
C
ILE
134
n
134
ILE
134
C
ALA
135
n
135
ALA
135
C
LEU
136
n
136
LEU
136
C
TRP
137
n
137
TRP
137
C
PHE
138
n
138
PHE
138
C
LYS
139
n
139
LYS
139
C
PRO
140
n
140
PRO
140
C
GLU
141
n
141
GLU
141
C
GLU
142
n
142
GLU
142
C
LEU
143
n
143
LEU
143
C
LEU
144
n
144
LEU
144
C
THR
145
n
145
THR
145
C
GLU
146
n
146
GLU
146
C
VAL
147
n
147
VAL
147
C
LYS
148
n
148
LYS
148
C
PRO
149
n
149
PRO
149
C
ASN
150
n
150
ASN
150
C
PRO
151
n
151
PRO
151
C
ASN
152
n
152
ASN
152
C
LEU
153
n
153
LEU
153
C
TYR
154
n
154
TYR
154
C
GLU
155
n
155
GLU
155
C
author_and_software_defined_assembly
PISA,PQS
6
hexameric
18360
-135
33890
A
RTP
160
E
O2A
RTP
1_555
A
MG
164
D
MG
MG
1_555
A
RTP
160
E
O1B
RTP
1_555
81.0
A
RTP
160
E
O2A
RTP
1_555
A
MG
164
D
MG
MG
1_555
A
RTP
160
E
O3G
RTP
1_555
71.8
A
RTP
160
E
O1B
RTP
1_555
A
MG
164
D
MG
MG
1_555
A
RTP
160
E
O3G
RTP
1_555
84.9
A
RTP
160
E
O2A
RTP
1_555
A
MG
164
D
MG
MG
1_555
A
HOH
1001
J
O
HOH
1_555
79.4
A
RTP
160
E
O1B
RTP
1_555
A
MG
164
D
MG
MG
1_555
A
HOH
1001
J
O
HOH
1_555
143.1
A
RTP
160
E
O3G
RTP
1_555
A
MG
164
D
MG
MG
1_555
A
HOH
1001
J
O
HOH
1_555
59.3
A
RTP
160
E
O2A
RTP
1_555
A
MG
164
D
MG
MG
1_555
A
HOH
1002
J
O
HOH
1_555
142.5
A
RTP
160
E
O1B
RTP
1_555
A
MG
164
D
MG
MG
1_555
A
HOH
1002
J
O
HOH
1_555
75.0
A
RTP
160
E
O3G
RTP
1_555
A
MG
164
D
MG
MG
1_555
A
HOH
1002
J
O
HOH
1_555
77.7
A
HOH
1001
J
O
HOH
1_555
A
MG
164
D
MG
MG
1_555
A
HOH
1002
J
O
HOH
1_555
103.3
A
RTP
160
E
O2A
RTP
1_555
A
MG
164
D
MG
MG
1_555
A
HOH
1003
J
O
HOH
1_555
108.9
A
RTP
160
E
O1B
RTP
1_555
A
MG
164
D
MG
MG
1_555
A
HOH
1003
J
O
HOH
1_555
74.6
A
RTP
160
E
O3G
RTP
1_555
A
MG
164
D
MG
MG
1_555
A
HOH
1003
J
O
HOH
1_555
158.9
A
HOH
1001
J
O
HOH
1_555
A
MG
164
D
MG
MG
1_555
A
HOH
1003
J
O
HOH
1_555
141.7
A
HOH
1002
J
O
HOH
1_555
A
MG
164
D
MG
MG
1_555
A
HOH
1003
J
O
HOH
1_555
92.1
A
RTP
161
F
O2A
RTP
1_555
B
MG
163
H
MG
MG
1_555
A
RTP
161
F
O3G
RTP
1_555
110.2
A
RTP
161
F
O2A
RTP
1_555
B
MG
163
H
MG
MG
1_555
A
RTP
161
F
O1B
RTP
1_555
70.8
A
RTP
161
F
O3G
RTP
1_555
B
MG
163
H
MG
MG
1_555
A
RTP
161
F
O1B
RTP
1_555
77.4
A
RTP
161
F
O2A
RTP
1_555
B
MG
163
H
MG
MG
1_555
A
HOH
1016
J
O
HOH
1_555
98.2
A
RTP
161
F
O3G
RTP
1_555
B
MG
163
H
MG
MG
1_555
A
HOH
1016
J
O
HOH
1_555
111.1
A
RTP
161
F
O1B
RTP
1_555
B
MG
163
H
MG
MG
1_555
A
HOH
1016
J
O
HOH
1_555
54.8
A
RTP
162
G
O3G
RTP
1_555
C
MG
165
I
MG
MG
1_555
A
RTP
162
G
O2A
RTP
1_555
64.3
A
RTP
162
G
O3G
RTP
1_555
C
MG
165
I
MG
MG
1_555
A
RTP
162
G
O1B
RTP
1_555
79.6
A
RTP
162
G
O2A
RTP
1_555
C
MG
165
I
MG
MG
1_555
A
RTP
162
G
O1B
RTP
1_555
75.5
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
-0.5000000000
-0.8660254038
0.0000000000
-0.8660254038
0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
6_765
-x+2,-x+y+1,-z+1/3
crystal symmetry operation
107.5965000000
62.1208682389
51.2726666667
A
N
VAL
38
A
N
VAL
38
A
O
GLU
83
A
O
GLU
83
A
O
MET
80
A
O
MET
80
A
N
LEU
13
A
N
LEU
13
A
N
ALA
14
A
N
ALA
14
A
O
GLY
122
A
O
GLY
122
B
N
GLY
41
B
N
GLY
41
B
O
VAL
81
B
O
VAL
81
B
O
MET
80
B
O
MET
80
B
N
LEU
13
B
N
LEU
13
B
N
ALA
14
B
N
ALA
14
B
O
GLY
122
B
O
GLY
122
C
N
GLY
41
C
N
GLY
41
C
O
VAL
81
C
O
VAL
81
C
O
MET
80
C
O
MET
80
C
N
LEU
13
C
N
LEU
13
C
N
ALA
14
C
N
ALA
14
C
O
GLY
122
C
O
GLY
122
1
A
MET
1
A
MET
1
1
Y
1
A
SER
2
A
SER
2
1
Y
1
A
THR
3
A
THR
3
1
Y
1
A
ASN
4
A
ASN
4
1
Y
1
A
LYS
5
A
LYS
5
1
Y
1
B
MET
1
B
MET
1
1
Y
1
B
SER
2
B
SER
2
1
Y
1
B
THR
3
B
THR
3
1
Y
1
B
ASN
4
B
ASN
4
1
Y
1
B
LYS
5
B
LYS
5
1
Y
1
C
MET
1
C
MET
1
1
Y
1
C
SER
2
C
SER
2
1
Y
1
C
THR
3
C
THR
3
1
Y
1
C
ASN
4
C
ASN
4
1
Y
1
C
LYS
5
C
LYS
5
1
Y
1
7.22
0.50
120.30
127.52
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
92
92
92
N
1
-7.65
0.50
120.30
112.65
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
92
92
92
N
1
-4.02
0.50
120.30
116.28
B
B
B
NE
CZ
NH1
ARG
ARG
ARG
92
92
92
N
1
4.18
0.50
120.30
124.48
B
B
B
NE
CZ
NH2
ARG
ARG
ARG
92
92
92
N
1
-3.76
0.50
120.30
116.54
C
C
C
NE
CZ
NH1
ARG
ARG
ARG
92
92
92
N
1
3.62
0.50
120.30
123.92
C
C
C
NE
CZ
NH2
ARG
ARG
ARG
92
92
92
N
1
A
ASN
7
-77.89
39.08
1
A
TYR
56
-89.62
31.41
1
A
LYS
60
-49.85
-16.34
1
A
PRO
63
-51.55
1.16
1
A
ILE
72
-48.97
-10.14
1
A
ILE
120
55.64
-48.51
1
A
ALA
130
-63.03
-71.27
1
B
ASP
50
-64.38
-70.12
1
B
ILE
72
-49.21
-11.06
1
B
VAL
114
-140.77
-17.85
1
B
ILE
120
54.24
-49.17
1
B
ALA
130
-62.93
-71.04
1
C
ASN
7
-150.13
81.38
1
C
GLU
9
-38.72
135.03
1
C
TYR
56
-88.72
31.74
1
C
ILE
72
-50.54
-9.72
1
C
ARG
118
-119.41
71.01
1
C
ILE
120
56.11
-49.52
1
C
ALA
130
-63.28
-71.86
1
C
PRO
151
-69.32
2.31
0.249
0.207
2.9
20.2
553
10647
10546
RANDOM
1
2.0
1.0
MOLECULAR REPLACEMENT
Engh & Huber
2.9
20.2
38
3548
90
0
3420
0.007
1.4
2.9
20.0
1MN9
10647
10546
2.0
1.0
1
99.1
2.9
3.0
10566
0.117
1
99.1
data reduction
DENZO
data scaling
SCALEPACK
phasing
AMoRE
refinement
CNS
1.0
NDP kinase mutant (H122G) complex with RTP
1
N
N
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
3
N
N
2
N
N
2
N
N
4
N
N
4
N
N
4
N
N
The biological assembly is a hexamer generated from the trimer
in the asymmetric unit
A
LYS
16
A
LYS
16
HELX_P
A
ARG
22
A
ARG
22
1
1
7
A
LEU
24
A
LEU
24
HELX_P
A
GLY
36
A
GLY
36
1
2
13
A
THR
48
A
THR
48
HELX_P
A
TYR
56
A
TYR
56
1
3
9
A
ALA
57
A
ALA
57
HELX_P
A
LYS
60
A
LYS
60
5
4
4
A
PHE
64
A
PHE
64
HELX_P
A
ILE
72
A
ILE
72
1
5
9
A
GLY
86
A
GLY
86
HELX_P
A
GLY
96
A
GLY
96
1
6
11
A
ASN
99
A
ASN
99
HELX_P
A
SER
103
A
SER
103
5
7
5
A
SER
107
A
SER
107
HELX_P
A
GLY
113
A
GLY
113
1
8
7
A
ASP
115
A
ASP
115
HELX_P
A
ASN
119
A
ASN
119
5
9
5
A
SER
126
A
SER
126
HELX_P
A
PHE
138
A
PHE
138
1
10
13
A
LYS
139
A
LYS
139
HELX_P
A
LEU
143
A
LEU
143
5
11
5
B
LYS
16
B
LYS
16
HELX_P
B
ARG
22
B
ARG
22
1
12
7
B
LEU
24
B
LEU
24
HELX_P
B
GLY
36
B
GLY
36
1
13
13
B
THR
48
B
THR
48
HELX_P
B
TYR
56
B
TYR
56
1
14
9
B
ALA
57
B
ALA
57
HELX_P
B
LYS
60
B
LYS
60
5
15
4
B
PHE
64
B
PHE
64
HELX_P
B
ILE
72
B
ILE
72
1
16
9
B
GLY
86
B
GLY
86
HELX_P
B
GLY
96
B
GLY
96
1
17
11
B
ASN
99
B
ASN
99
HELX_P
B
SER
103
B
SER
103
5
18
5
B
SER
107
B
SER
107
HELX_P
B
GLY
113
B
GLY
113
1
19
7
B
SER
126
B
SER
126
HELX_P
B
PHE
138
B
PHE
138
1
20
13
B
LYS
139
B
LYS
139
HELX_P
B
LEU
143
B
LEU
143
5
21
5
C
LYS
16
C
LYS
16
HELX_P
C
ARG
22
C
ARG
22
1
22
7
C
LEU
24
C
LEU
24
HELX_P
C
GLY
36
C
GLY
36
1
23
13
C
THR
48
C
THR
48
HELX_P
C
TYR
56
C
TYR
56
1
24
9
C
ALA
57
C
ALA
57
HELX_P
C
LYS
60
C
LYS
60
5
25
4
C
PHE
64
C
PHE
64
HELX_P
C
ILE
72
C
ILE
72
1
26
9
C
GLY
86
C
GLY
86
HELX_P
C
GLY
96
C
GLY
96
1
27
11
C
ASN
99
C
ASN
99
HELX_P
C
SER
103
C
SER
103
5
28
5
C
SER
107
C
SER
107
HELX_P
C
GLY
113
C
GLY
113
1
29
7
C
SER
126
C
SER
126
HELX_P
C
PHE
138
C
PHE
138
1
30
13
C
LYS
139
C
LYS
139
HELX_P
C
LEU
143
C
LEU
143
5
31
5
metalc
2.168
A
RTP
160
E
O2A
RTP
1_555
A
MG
164
D
MG
MG
1_555
metalc
2.407
A
RTP
160
E
O1B
RTP
1_555
A
MG
164
D
MG
MG
1_555
metalc
2.780
A
RTP
160
E
O3G
RTP
1_555
A
MG
164
D
MG
MG
1_555
metalc
1.888
A
RTP
161
F
O2A
RTP
1_555
B
MG
163
H
MG
MG
1_555
metalc
1.991
A
RTP
161
F
O3G
RTP
1_555
B
MG
163
H
MG
MG
1_555
metalc
2.826
A
RTP
161
F
O1B
RTP
1_555
B
MG
163
H
MG
MG
1_555
metalc
2.677
A
RTP
162
G
O3G
RTP
1_555
C
MG
165
I
MG
MG
1_555
metalc
2.260
A
RTP
162
G
O2A
RTP
1_555
C
MG
165
I
MG
MG
1_555
metalc
2.460
A
RTP
162
G
O1B
RTP
1_555
C
MG
165
I
MG
MG
1_555
metalc
1.920
A
MG
164
D
MG
MG
1_555
A
HOH
1001
J
O
HOH
1_555
metalc
2.013
A
MG
164
D
MG
MG
1_555
A
HOH
1002
J
O
HOH
1_555
metalc
1.938
A
MG
164
D
MG
MG
1_555
A
HOH
1003
J
O
HOH
1_555
metalc
1.901
A
HOH
1016
J
O
HOH
1_555
B
MG
163
H
MG
MG
1_555
TRANSFERASE
NDP kinase-Ribavirin complex, transferase
NDKC_DICDI
UNP
1
1
P22887
MSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAM
VFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE
1
155
1MN9
1
155
P22887
A
1
1
155
1
155
1MN9
1
155
P22887
B
1
1
155
1
155
1MN9
1
155
P22887
C
1
1
155
1
HIS
engineered mutation
GLY
122
1MN9
A
P22887
UNP
122
122
2
HIS
engineered mutation
GLY
122
1MN9
B
P22887
UNP
122
122
3
HIS
engineered mutation
GLY
122
1MN9
C
P22887
UNP
122
122
4
4
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
VAL
38
A
VAL
38
A
LEU
45
A
LEU
45
A
VAL
77
A
VAL
77
A
GLU
83
A
GLU
83
A
ARG
10
A
ARG
10
A
VAL
15
A
VAL
15
A
ILE
121
A
ILE
121
A
GLY
123
A
GLY
123
B
VAL
38
B
VAL
38
B
LEU
45
B
LEU
45
B
VAL
77
B
VAL
77
B
GLU
83
B
GLU
83
B
ARG
10
B
ARG
10
B
VAL
15
B
VAL
15
B
ILE
121
B
ILE
121
B
GLY
123
B
GLY
123
C
VAL
38
C
VAL
38
C
LEU
45
C
LEU
45
C
VAL
77
C
VAL
77
C
GLU
83
C
GLU
83
C
ARG
10
C
ARG
10
C
VAL
15
C
VAL
15
C
ILE
121
C
ILE
121
C
GLY
123
C
GLY
123
BINDING SITE FOR RESIDUE MG B 163
B
MG
163
Software
2
BINDING SITE FOR RESIDUE MG A 164
A
MG
164
Software
4
BINDING SITE FOR RESIDUE MG C 165
C
MG
165
Software
2
BINDING SITE FOR RESIDUE RTP A 160
A
RTP
160
Software
16
BINDING SITE FOR RESIDUE RTP A 161
A
RTP
161
Software
14
BINDING SITE FOR RESIDUE RTP A 162
A
RTP
162
Software
13
A
RTP
161
F
RTP
2
1_555
A
HOH
1016
J
HOH
2
1_555
A
RTP
160
E
RTP
4
1_555
A
HOH
1001
J
HOH
4
1_555
A
HOH
1002
J
HOH
4
1_555
A
HOH
1003
J
HOH
4
1_555
A
RTP
162
G
RTP
2
1_555
C
ASP
125
C
ASP
125
2
1_555
A
LYS
16
A
LYS
16
16
1_555
A
TYR
56
A
TYR
56
16
1_555
A
HIS
59
A
HIS
59
16
1_555
A
PHE
64
A
PHE
64
16
1_555
A
LEU
68
A
LEU
68
16
1_555
A
ARG
92
A
ARG
92
16
1_555
A
THR
98
A
THR
98
16
1_555
A
ARG
109
A
ARG
109
16
1_555
A
VAL
116
A
VAL
116
16
1_555
A
ASN
119
A
ASN
119
16
1_555
A
GLY
122
A
GLY
122
16
1_555
A
GLY
123
A
GLY
123
16
1_555
A
MG
164
D
MG
16
1_555
A
HOH
1001
J
HOH
16
1_555
A
HOH
1002
J
HOH
16
1_555
A
HOH
1003
J
HOH
16
1_555
A
HOH
1016
J
HOH
14
1_555
B
LYS
16
B
LYS
16
14
1_555
B
TYR
56
B
TYR
56
14
1_555
B
HIS
59
B
HIS
59
14
1_555
B
PHE
64
B
PHE
64
14
1_555
B
LEU
68
B
LEU
68
14
1_555
B
ARG
92
B
ARG
92
14
1_555
B
THR
98
B
THR
98
14
1_555
B
ARG
109
B
ARG
109
14
1_555
B
VAL
116
B
VAL
116
14
1_555
B
ASN
119
B
ASN
119
14
1_555
B
GLY
122
B
GLY
122
14
1_555
B
GLY
123
B
GLY
123
14
1_555
B
MG
163
H
MG
14
1_555
C
LYS
16
C
LYS
16
13
1_555
C
TYR
56
C
TYR
56
13
1_555
C
HIS
59
C
HIS
59
13
1_555
C
PHE
64
C
PHE
64
13
1_555
C
LEU
68
C
LEU
68
13
1_555
C
ARG
92
C
ARG
92
13
1_555
C
THR
98
C
THR
98
13
1_555
C
ARG
109
C
ARG
109
13
1_555
C
VAL
116
C
VAL
116
13
1_555
C
ASN
119
C
ASN
119
13
1_555
C
GLY
122
C
GLY
122
13
1_555
C
GLY
123
C
GLY
123
13
1_555
C
MG
165
I
MG
13
1_555
152
P 31 2 1