1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Ho, W.C.
Steinbeck, C.
Richert, C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C10 H15 N3 O4
241.244
n
5'-AMINO-5'-DEOXYTHYMIDINE
DNA linking
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
N
1
N
N
N
2
N
N
N
3
N
C
N
4
N
C
N
5
N
O
N
6
N
N
N
7
N
C
N
8
N
O
N
9
N
C
N
10
N
C
N
11
N
C
N
12
N
C
N
13
R
C
N
14
N
O
N
15
R
C
N
16
S
C
N
17
N
O
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
H
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
O
N
34
N
P
N
35
N
O
N
36
N
O
N
37
N
O
N
38
N
C
N
39
R
C
N
40
N
O
N
41
S
C
N
42
N
O
N
43
N
C
N
44
R
C
Y
45
N
N
Y
46
N
C
Y
47
N
N
Y
48
N
C
Y
49
N
C
N
50
N
N
Y
51
N
N
Y
52
N
C
Y
53
N
N
Y
54
N
C
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
O
N
70
N
P
N
71
N
O
N
72
N
O
N
73
N
O
N
74
N
C
N
75
R
C
N
76
N
O
N
77
S
C
N
78
N
O
N
79
N
C
N
80
R
C
N
81
N
N
N
82
N
C
N
83
N
O
N
84
N
N
N
85
N
C
N
86
N
N
N
87
N
C
N
88
N
C
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
O
N
104
N
P
N
105
N
O
N
106
N
O
N
107
N
O
N
108
N
C
N
109
R
C
N
110
N
O
N
111
S
C
N
112
N
O
N
113
N
C
N
114
R
C
Y
115
N
N
Y
116
N
C
Y
117
N
N
Y
118
N
C
N
119
N
C
N
120
N
O
N
121
N
N
N
122
N
C
N
123
N
N
N
124
N
N
Y
125
N
C
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
N
N
141
S
C
N
142
N
C
N
143
N
O
N
144
N
C
Y
145
N
C
Y
146
N
C
Y
147
N
C
Y
148
N
N
Y
149
N
C
Y
150
N
C
Y
151
N
C
Y
152
N
C
Y
153
N
C
N
154
N
O
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
doub
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
doub
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
doub
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
Y
57
N
sing
Y
58
N
sing
Y
59
N
doub
N
60
N
sing
Y
61
N
sing
Y
62
N
sing
Y
63
N
doub
N
64
N
sing
Y
65
N
doub
N
66
N
sing
N
67
N
sing
Y
68
N
sing
Y
69
N
doub
N
70
N
sing
Y
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
doub
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
doub
N
98
N
sing
N
99
N
doub
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
Y
130
N
sing
Y
131
N
sing
Y
132
N
doub
N
133
N
sing
Y
134
N
sing
N
135
N
sing
Y
136
N
doub
N
137
N
doub
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
doub
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
Y
157
N
doub
Y
158
N
sing
Y
159
N
sing
N
160
N
sing
Y
161
N
doub
Y
162
N
sing
Y
163
N
sing
N
164
N
sing
Y
165
N
sing
Y
166
N
doub
N
167
N
sing
Y
168
N
doub
N
169
N
sing
Y
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
38
12597
12606
10.1021/bi991169w
10504228
Solution structure of the aminoacyl-capped oligodeoxyribonucleotide duplex (W-TGCGCAC)(2).
1999
10.2210/pdb1c95/pdb
pdb_00001c95
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
2017.435
5'-D((5AT)TP*GP*CP*GP*CP*AP*C)-3'
2
syn
polymer
204.225
TRYPTOPHAN
2
syn
non-polymer
no
yes
(5AT)(DG)(DC)(DG)(DC)(DA)(DC)
TGCGCAC
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
-8.003
1
20
A
1
B
6
-0.164
A_5AT1:DA6_B
1
-9.557
-0.059
0.323
-0.264
-2.850
1
19
A
2
B
5
0.823
A_DG2:DC5_B
2
-15.797
-0.543
0.051
-0.268
-3.281
1
19
A
3
B
4
-9.499
A_DC3:DG4_B
3
20.493
0.260
-0.729
-0.413
2.641
1
19
A
4
B
3
-9.722
A_DG4:DC3_B
4
21.305
-0.168
-0.762
-0.403
3.294
1
19
A
5
B
2
1.758
A_DC5:DG2_B
5
-13.630
0.694
-0.090
-0.316
8.602
1
20
A
6
B
1
-1.803
A_DA6:5AT1_B
6
-10.888
0.259
0.342
-0.241
3.498
44.355
A
A
1
2
3.280
B
B
6
5
3.338
2.474
0.512
2.726
AA_5AT1DG2:DC5DA6_BB
1
2.262
-2.999
44.234
3.370
-0.458
3.949
37.118
A
A
2
3
4.925
B
B
5
4
3.809
3.131
-0.118
1.865
AA_DG2DC3:DG4DC5_BB
2
-1.854
2.917
36.945
2.433
-0.109
3.827
37.862
A
A
3
4
18.625
B
B
4
3
3.479
11.895
-0.004
1.689
AA_DC3DG4:DC3DG4_BB
3
0.126
-0.198
36.010
0.851
0.024
3.963
36.941
A
A
4
5
5.510
B
B
3
2
3.802
3.484
0.218
1.872
AA_DG4DC5:DG2DC3_BB
4
2.325
-3.677
36.711
2.395
0.030
3.714
45.306
A
A
5
6
7.897
B
B
2
1
3.383
6.062
-0.614
2.544
AA_DC5DA6:5AT1DG2_BB
5
-3.371
4.392
44.799
2.715
0.470
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Data collection
1
0
1999-10-08
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-16
1
4
2024-05-22
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
1999-07-31
REL
TRP
TRYPTOPHAN
CONSTRAINTS WERE GENERATED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.
1
2D NOESY
DQF-COSY
TOCSY
2D NOESY
160 mM
7
AMBIENT
283
K
160 mM
7
AMBIENT
283
K
SEE TABLE 5 IN PAPER
TORSION-ANGLE MOLECULAR DYNAMICS FOLLOWED BY CARTESIAN MOLECULAR DYNAMICS
1
lowest energy
4 MM TRP-TGCGCAC IN 150 MM NACL AND 10 MM PHOSPHATE BUFFER (KH2PO4/K2HPO4) AT PH 7.0 (UNCORRECTED FOR DEUTERIUM EFFECT)
4 MM TRP-TGCGCAC IN 150 MM NACL AND 10 MM PHOSPHATE BUFFER (KH2PO4/K2HPO4) AT PH 7.0 (UNCORRECTED FOR DEUTERIUM EFFECT)
RUBEN, D. ET AL. (MIT BITTER LABS)
collection
RNMR
1998
BRUKER
collection
XwinNMR
1998
MARC-ANDRE' DELSUC, MONTPELLIER, FRANCE
data analysis
Gifa
4.10
BRUENGER, A.; GROSSE-KUNSTLEVE, R.W. ET AL.; YALE UNIVERSITY
structure solution
CNS
0.4
BRUENGER, A., ET AL. YALE UNIVERSITY
refinement
X-PLOR
3.1
500
MIT-BUILT
750
MIT-BUILT
600
Bruker
DRX
300
Bruker
DPX
TRP
0
2
TRP
TRP
0
A
TRP
0
2
TRP
TRP
0
B
5AT
1
n
1
5AT
1
A
DG
2
n
2
DG
2
A
DC
3
n
3
DC
3
A
DG
4
n
4
DG
4
A
DC
5
n
5
DC
5
A
DA
6
n
6
DA
6
A
DC
7
n
7
DC
7
A
5AT
1
n
1
5AT
1
B
DG
2
n
2
DG
2
B
DC
3
n
3
DC
3
B
DG
4
n
4
DG
4
B
DC
5
n
5
DC
5
B
DA
6
n
6
DA
6
B
DC
7
n
7
DC
7
B
author_defined_assembly
2
dimeric
A
5AT
1
5'-AMINO-5'-DEOXYTHYMIDINE
A
5AT
1
DT
B
5AT
1
5'-AMINO-5'-DEOXYTHYMIDINE
B
5AT
1
DT
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
Solution structure of the aminoacyl-capped oligodeoxyribonucleotide duplex TRP-D(TGCGCAC)2
1
N
N
1
N
N
2
N
N
2
N
N
covale
1.334
one
A
TRP
0
C
C
TRP
1_555
A
5AT
1
A
N5'
5AT
1
1_555
covale
1.608
both
A
5AT
1
A
O3'
5AT
1
1_555
A
DG
2
A
P
DG
2
1_555
covale
1.334
one
B
TRP
0
D
C
TRP
1_555
B
5AT
1
B
N5'
5AT
1
1_555
covale
1.608
both
B
5AT
1
B
O3'
5AT
1
1_555
B
DG
2
B
P
DG
2
1_555
hydrog
WATSON-CRICK
A
5AT
1
A
N3
5AT
1
1_555
B
DA
6
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
5AT
1
A
O4
5AT
1
1_555
B
DA
6
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
5
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
5
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
5
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
4
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
4
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
4
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
3
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
3
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
3
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
2
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
2
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
2
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
5AT
1
B
N3
5AT
1
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
5AT
1
B
O4
5AT
1
1_555
DNA
DOUBLE HELIX, Aminoacyl-Capped DNA, DNA
1C95
PDB
1
1C95
1
7
1C95
1
7
1C95
A
1
1
7
1
7
1C95
1
7
1C95
B
1
1
7
BINDING SITE FOR RESIDUE TRP A 0
A
TRP
0
Software
2
BINDING SITE FOR RESIDUE TRP B 0
B
TRP
0
Software
2
A
5AT
1
A
5AT
1
2
1_555
B
DA
6
B
DA
6
2
1_555
A
DA
6
A
DA
6
2
1_555
B
5AT
1
B
5AT
1
2
1_555