1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Demene, H.
Morellet, N.
Teilleux, V.
Huynh-Dinh, T.
De Rocquigny, H.
Fournie-Zaluski, M.C.
Roques, B.P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
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
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 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
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
Zn 2
65.409
ZINC ION
non-polymer
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
283
419
434
10.1006/jmbi.1998.2098
9769215
Structure of the complex between the HIV-1 nucleocapsid protein NCp7 and the single-stranded pentanucleotide d(ACGCC).
1998
10.2210/pdb1bj6/pdb
pdb_00001bj6
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1465.001
DNA (5'-D(*AP*CP*GP*CP*C)-3')
1
syn
polymer
4837.642
NUCLEOCAPSID PROTEIN 7
RESIDUES 12-53
1
man
polymer
65.409
ZINC ION
2
syn
non-polymer
(12-53)NCP7
no
no
(DA)(DC)(DG)(DC)(DC)
ACGCC
D
polydeoxyribonucleotide
no
no
NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQ
NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQ
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
Lentivirus
MAL
sample
11676
Human immunodeficiency virus 1
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Other
1
0
1999-02-02
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_pdbx_nmr_software.name
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr2_PDB_ins_code
_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_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_ins_code
_struct_site.pdbx_auth_seq_id
Y
BNL
1998-07-03
REL
ZN
ZINC ION
LEAST RESTRAINT VIOLATION AND LOWEST TOTAL ENERGY
50
10
NOESY
TOCSY
DQF
LOW SALT CONDITIONS
6.0
1
atm
303
K
THE PROTEIN PART OF THE STRUCTURE WAS FIRST GENERATED USING A RESTRAINTED DYNAMICAL ANNEALING CALCULATION. THE D(ACGCC) NUCLEIC ACID UNDER A DNA CONFORMATION WAS DOCKED APPROXIMATIVELY TO THE PROTEIN BASED ON THE 28 INTERMOLECULAR NOES. THE DOCKED STRUCTURE WAS ENERGY-MINIMIZED UNDER NOES RESTRAINTS. THIS INITIAL COMPLEXED STRUCTURE WAS THEN USED FOR A SECOND SET OF SIMULATED ANNEALING CALCULATION.
DYNAMICAL SIMULATED ANNEALING
WATER
BIOSYM
refinement
Discover
structure solution
BRUKER DISNMR
DISNMR
structure solution
BIOSYM/MSI
600
Bruker
AMX600
ZN
54
3
ZN
H
ZN
54
A
ZN
55
3
ZN
H
ZN
55
A
A
1
n
1
DA
1
D
C
2
n
2
DC
2
D
G
3
n
3
DG
3
D
C
4
n
4
DC
4
D
C
5
n
5
DC
5
D
ASN
12
n
1
ASN
12
A
VAL
13
n
2
VAL
13
A
LYS
14
n
3
LYS
14
A
CYS
15
n
4
CYS
15
A
PHE
16
n
5
PHE
16
A
ASN
17
n
6
ASN
17
A
CYS
18
n
7
CYS
18
A
GLY
19
n
8
GLY
19
A
LYS
20
n
9
LYS
20
A
GLU
21
n
10
GLU
21
A
GLY
22
n
11
GLY
22
A
HIS
23
n
12
HIS
23
A
THR
24
n
13
THR
24
A
ALA
25
n
14
ALA
25
A
ARG
26
n
15
ARG
26
A
ASN
27
n
16
ASN
27
A
CYS
28
n
17
CYS
28
A
ARG
29
n
18
ARG
29
A
ALA
30
n
19
ALA
30
A
PRO
31
n
20
PRO
31
A
ARG
32
n
21
ARG
32
A
LYS
33
n
22
LYS
33
A
LYS
34
n
23
LYS
34
A
GLY
35
n
24
GLY
35
A
CYS
36
n
25
CYS
36
A
TRP
37
n
26
TRP
37
A
LYS
38
n
27
LYS
38
A
CYS
39
n
28
CYS
39
A
GLY
40
n
29
GLY
40
A
LYS
41
n
30
LYS
41
A
GLU
42
n
31
GLU
42
A
GLY
43
n
32
GLY
43
A
HIS
44
n
33
HIS
44
A
GLN
45
n
34
GLN
45
A
MET
46
n
35
MET
46
A
LYS
47
n
36
LYS
47
A
ASP
48
n
37
ASP
48
A
CYS
49
n
38
CYS
49
A
THR
50
n
39
THR
50
A
GLU
51
n
40
GLU
51
A
ARG
52
n
41
ARG
52
A
GLN
53
n
42
GLN
53
A
author_defined_assembly
2
dimeric
A
CYS
15
B
SG
CYS
4
1_555
H
A
ZN
54
C
ZN
ZN
1_555
A
CYS
18
B
SG
CYS
7
1_555
114.9
A
CYS
15
B
SG
CYS
4
1_555
H
A
ZN
54
C
ZN
ZN
1_555
A
HIS
23
B
NE2
HIS
12
1_555
105.4
A
CYS
18
B
SG
CYS
7
1_555
H
A
ZN
54
C
ZN
ZN
1_555
A
HIS
23
B
NE2
HIS
12
1_555
109.4
A
CYS
15
B
SG
CYS
4
1_555
H
A
ZN
54
C
ZN
ZN
1_555
A
CYS
28
B
SG
CYS
17
1_555
109.9
A
CYS
18
B
SG
CYS
7
1_555
H
A
ZN
54
C
ZN
ZN
1_555
A
CYS
28
B
SG
CYS
17
1_555
107.9
A
HIS
23
B
NE2
HIS
12
1_555
H
A
ZN
54
C
ZN
ZN
1_555
A
CYS
28
B
SG
CYS
17
1_555
109.2
A
CYS
36
B
SG
CYS
25
1_555
H
A
ZN
55
D
ZN
ZN
1_555
A
CYS
39
B
SG
CYS
28
1_555
113.9
A
CYS
36
B
SG
CYS
25
1_555
H
A
ZN
55
D
ZN
ZN
1_555
A
HIS
44
B
NE2
HIS
33
1_555
106.0
A
CYS
39
B
SG
CYS
28
1_555
H
A
ZN
55
D
ZN
ZN
1_555
A
HIS
44
B
NE2
HIS
33
1_555
108.0
A
CYS
36
B
SG
CYS
25
1_555
H
A
ZN
55
D
ZN
ZN
1_555
A
CYS
49
B
SG
CYS
38
1_555
106.8
A
CYS
39
B
SG
CYS
28
1_555
H
A
ZN
55
D
ZN
ZN
1_555
A
CYS
49
B
SG
CYS
38
1_555
112.4
A
HIS
44
B
NE2
HIS
33
1_555
H
A
ZN
55
D
ZN
ZN
1_555
A
CYS
49
B
SG
CYS
38
1_555
109.4
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
1
D
DG
3
0.062
SIDE CHAIN
5
D
DC
2
0.094
SIDE CHAIN
8
D
DC
2
0.091
SIDE CHAIN
9
D
DC
5
0.074
SIDE CHAIN
10
A
ARG
52
0.090
SIDE CHAIN
1
3.86
0.60
118.90
122.76
D
D
D
N1
C2
O2
DC
DC
DC
2
2
2
N
1
2.78
0.30
108.30
111.08
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
2
-5.08
0.70
102.20
97.12
D
D
D
C4'
C3'
C2'
DA
DA
DA
1
1
1
N
2
3.09
0.30
108.30
111.39
D
D
D
O4'
C1'
N9
DA
DA
DA
1
1
1
N
2
3.08
0.30
108.30
111.38
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
3
2.65
0.30
108.30
110.95
D
D
D
O4'
C1'
N1
DC
DC
DC
2
2
2
N
3
3.37
0.30
108.30
111.67
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
3
2.63
0.30
108.30
110.93
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
4
3.70
0.30
108.30
112.00
D
D
D
O4'
C1'
N9
DA
DA
DA
1
1
1
N
4
3.66
0.30
108.30
111.96
D
D
D
O4'
C1'
N1
DC
DC
DC
2
2
2
N
4
4.37
0.30
108.30
112.67
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
4
3.07
0.30
108.30
111.37
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
5
3.77
0.30
108.30
112.07
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
6
2.30
0.30
108.30
110.60
D
D
D
O4'
C1'
N1
DC
DC
DC
2
2
2
N
6
4.54
0.30
108.30
112.84
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
6
3.88
0.30
108.30
112.18
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
7
-4.34
0.70
102.20
97.86
D
D
D
C4'
C3'
C2'
DA
DA
DA
1
1
1
N
7
4.29
0.30
108.30
112.59
D
D
D
O4'
C1'
N9
DA
DA
DA
1
1
1
N
7
4.01
0.60
118.90
122.91
D
D
D
N1
C2
O2
DC
DC
DC
2
2
2
N
7
2.47
0.30
108.30
110.77
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
7
2.30
0.30
108.30
110.60
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
8
5.95
0.30
108.30
114.25
D
D
D
O4'
C1'
N9
DA
DA
DA
1
1
1
N
8
4.53
0.30
108.30
112.83
D
D
D
O4'
C1'
N1
DC
DC
DC
2
2
2
N
8
3.80
0.30
108.30
112.10
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
8
2.41
0.30
108.30
110.71
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
9
3.96
0.30
108.30
112.26
D
D
D
O4'
C1'
N9
DA
DA
DA
1
1
1
N
9
4.42
0.30
108.30
112.72
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
9
3.45
0.30
108.30
111.75
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
10
-4.62
0.70
102.20
97.58
D
D
D
C4'
C3'
C2'
DA
DA
DA
1
1
1
N
10
3.90
0.30
108.30
112.20
D
D
D
O4'
C1'
N9
DA
DA
DA
1
1
1
N
10
2.19
0.30
108.30
110.49
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
1
A
ASN
17
-143.86
-85.72
1
A
THR
50
-161.23
28.65
2
A
CYS
15
-33.96
117.55
2
A
ASN
17
-82.29
-88.64
2
A
THR
50
-172.92
40.68
2
A
GLU
51
-14.51
-81.19
3
A
LYS
14
-163.23
67.84
3
A
CYS
15
-0.79
111.70
3
A
ASN
17
-155.66
-64.58
3
A
HIS
44
-160.04
-161.19
3
A
THR
50
-179.33
37.32
3
A
GLU
51
-17.62
-78.97
3
A
ARG
52
29.50
40.55
4
A
ASN
17
-75.05
-77.67
4
A
LYS
38
-56.19
-76.43
4
A
THR
50
-165.18
29.80
4
A
ARG
52
25.12
67.85
5
A
VAL
13
-139.07
-57.21
5
A
LYS
14
76.92
105.20
5
A
PHE
16
-79.62
48.99
5
A
ASN
17
-151.54
-74.27
5
A
LYS
38
-56.15
-71.83
5
A
HIS
44
-103.60
-160.84
5
A
THR
50
-177.15
36.22
5
A
GLU
51
-22.36
-76.29
5
A
ARG
52
56.40
74.27
6
A
CYS
15
-28.88
121.74
6
A
PHE
16
-83.92
49.25
6
A
ASN
17
-152.33
-77.47
6
A
HIS
44
-97.03
-148.58
6
A
THR
50
-160.90
38.04
6
A
ARG
52
-66.60
-152.65
7
A
PHE
16
-91.44
39.21
7
A
ASN
17
-148.06
-75.41
7
A
THR
50
-152.14
25.47
7
A
GLU
51
-91.45
-120.10
7
A
ARG
52
156.21
134.69
8
A
ASN
17
-149.44
-80.14
8
A
THR
50
-177.99
36.70
8
A
GLU
51
-7.06
-80.12
9
A
CYS
15
-34.95
124.00
9
A
ASN
17
-154.88
-83.80
9
A
THR
50
-141.97
19.07
9
A
ARG
52
-163.77
85.87
10
A
CYS
15
-21.44
114.95
10
A
ASN
17
-151.95
-73.79
10
A
LYS
38
-57.14
-74.14
10
A
HIS
44
-116.76
-162.78
10
A
ARG
52
-169.22
79.12
1H NMR OF (12-53) NCP7/D(ACGCC) COMPLEX, 10 STRUCTURES
1
N
N
2
N
N
3
N
N
3
N
N
metalc
2.312
H
A
CYS
15
B
SG
CYS
4
1_555
A
ZN
54
C
ZN
ZN
1_555
metalc
2.255
H
A
CYS
18
B
SG
CYS
7
1_555
A
ZN
54
C
ZN
ZN
1_555
metalc
2.037
H
A
HIS
23
B
NE2
HIS
12
1_555
A
ZN
54
C
ZN
ZN
1_555
metalc
2.229
H
A
CYS
28
B
SG
CYS
17
1_555
A
ZN
54
C
ZN
ZN
1_555
metalc
2.303
H
A
CYS
36
B
SG
CYS
25
1_555
A
ZN
55
D
ZN
ZN
1_555
metalc
2.266
H
A
CYS
39
B
SG
CYS
28
1_555
A
ZN
55
D
ZN
ZN
1_555
metalc
2.025
H
A
HIS
44
B
NE2
HIS
33
1_555
A
ZN
55
D
ZN
ZN
1_555
metalc
2.267
H
A
CYS
49
B
SG
CYS
38
1_555
A
ZN
55
D
ZN
ZN
1_555
Viral protein/DNA
COMPLEX (NUCLEOCAPSID PROTEIN-DNA), NUCLEIC ACID, RETROVIRUS, VIRUS MORPHOGENESIS, ZINC FINGER, Viral protein-DNA COMPLEX
Q74084_9HIV1
UNP
2
390
Q74084
1BJ6
PDB
1
1BJ6
390
430
1BJ6
13
53
Q74084
A
1
2
42
1
5
1BJ6
1
5
1BJ6
D
2
1
5
ZINC-BINDING SITES.
Unknown
7
BINDING SITE FOR RESIDUE ZN A 54H
A
ZN
H
54
Software
4
BINDING SITE FOR RESIDUE ZN A 55H
A
ZN
H
55
Software
4
A
CYS
15
B
CYS
4
7
1_555
A
CYS
18
B
CYS
7
7
1_555
A
HIS
23
B
HIS
12
7
1_555
A
CYS
28
B
CYS
17
7
1_555
A
CYS
36
B
CYS
25
7
1_555
A
CYS
39
B
CYS
28
7
1_555
A
HIS
44
B
HIS
33
7
1_555
A
CYS
15
B
CYS
4
4
1_555
A
CYS
18
B
CYS
7
4
1_555
A
HIS
23
B
HIS
12
4
1_555
A
CYS
28
B
CYS
17
4
1_555
A
CYS
36
B
CYS
25
4
1_555
A
CYS
39
B
CYS
28
4
1_555
A
HIS
44
B
HIS
33
4
1_555
A
CYS
49
B
CYS
38
4
1_555
1
P 1