1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
South, T.L.
Summers, M.F.
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
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 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 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
Zn 2
65.409
ZINC ION
non-polymer
US
Protein Sci.
PRCIEI
0795
0961-8368
2
3
8443588
Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger of the HIV-1 nucleocapsid protein: NMR structure of the complex with the Psi-site analog, dACGCC.
1993
US
Protein Sci.
PRCIEI
0795
0961-8368
1
563
Nucleocapsid Zinc Fingers Detected in Retroviruses: Exafs Studies of Intact Viruses and the Solution-State Structure of the Nucleocapsid Protein from HIV-1
1992
US
Biochemistry
BICHAW
0033
0006-2960
30
6342
The C-Terminal Retroviral-Type Zinc Finger Domain from the HIV-1 Nucleocapsid Protein is Structurally Similar to the N-Terminal Zinc Finger Domain
1991
US
Biochemistry
BICHAW
0033
0006-2960
29
7786
The Nucleocapsid Protein Isolated from HIV-I Particles Binds Zinc and Form Retroviral-Type Zinc Fingers
1990
10.2210/pdb1hvn/pdb
pdb_00001hvn
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(P*AP*CP*GP*CP*C)-3')
1
syn
polymer
2011.379
Hiv-1 Nucleocapsid Zinc Finger
1
man
polymer
65.409
ZINC ION
1
syn
non-polymer
no
no
(DA)(DC)(DG)(DC)(DC)
ACGCC
D
polydeoxyribonucleotide
no
no
VKCFNCGKEGHIARNCRA
VKCFNCGKEGHIARNCRA
E
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
Lentivirus
sample
11676
Human immunodeficiency virus 1
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_conn_angle
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1994-01-31
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_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_seq_id
Y
BNL
1992-12-08
REL
ZN
ZINC ION
15
ZN
19
3
ZN
ZN
19
E
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
VAL
1
n
1
VAL
1
E
LYS
2
n
2
LYS
2
E
CYS
3
n
3
CYS
3
E
PHE
4
n
4
PHE
4
E
ASN
5
n
5
ASN
5
E
CYS
6
n
6
CYS
6
E
GLY
7
n
7
GLY
7
E
LYS
8
n
8
LYS
8
E
GLU
9
n
9
GLU
9
E
GLY
10
n
10
GLY
10
E
HIS
11
n
11
HIS
11
E
ILE
12
n
12
ILE
12
E
ALA
13
n
13
ALA
13
E
ARG
14
n
14
ARG
14
E
ASN
15
n
15
ASN
15
E
CYS
16
n
16
CYS
16
E
ARG
17
n
17
ARG
17
E
ALA
18
n
18
ALA
18
E
author_defined_assembly
2
dimeric
E
CYS
3
B
SG
CYS
3
1_555
E
ZN
19
C
ZN
ZN
1_555
E
CYS
6
B
SG
CYS
6
1_555
106.3
E
CYS
3
B
SG
CYS
3
1_555
E
ZN
19
C
ZN
ZN
1_555
E
HIS
11
B
NE2
HIS
11
1_555
92.9
E
CYS
6
B
SG
CYS
6
1_555
E
ZN
19
C
ZN
ZN
1_555
E
HIS
11
B
NE2
HIS
11
1_555
109.3
E
CYS
3
B
SG
CYS
3
1_555
E
ZN
19
C
ZN
ZN
1_555
E
CYS
16
B
SG
CYS
16
1_555
115.0
E
CYS
6
B
SG
CYS
6
1_555
E
ZN
19
C
ZN
ZN
1_555
E
CYS
16
B
SG
CYS
16
1_555
108.9
E
HIS
11
B
NE2
HIS
11
1_555
E
ZN
19
C
ZN
ZN
1_555
E
CYS
16
B
SG
CYS
16
1_555
122.7
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
E
CYS
3
-13.76
1
E
PHE
4
-10.95
1
E
ILE
12
-13.16
2
E
CYS
3
-12.83
2
E
HIS
11
11.54
2
E
ILE
12
-14.39
2
E
ARG
17
10.45
3
E
CYS
3
-12.22
3
E
PHE
4
-10.09
3
E
HIS
11
13.00
3
E
ILE
12
-13.84
4
E
CYS
3
-11.75
4
E
ILE
12
-13.80
5
E
CYS
3
-10.93
5
E
ILE
12
-14.01
6
E
CYS
3
-11.92
6
E
ILE
12
-15.55
7
E
CYS
3
-11.22
7
E
ILE
12
-13.93
7
E
CYS
16
13.19
8
E
VAL
1
-12.01
8
E
HIS
11
11.73
8
E
ILE
12
-16.01
9
E
CYS
3
-11.10
9
E
ILE
12
-15.33
10
E
CYS
3
-12.07
10
E
HIS
11
12.37
10
E
ILE
12
-13.94
11
E
CYS
3
-13.08
11
E
HIS
11
10.80
11
E
ILE
12
-15.39
12
E
CYS
3
-13.40
12
E
HIS
11
11.02
12
E
ILE
12
-15.14
13
E
CYS
3
-14.24
13
E
ASN
5
-10.39
13
E
HIS
11
10.38
13
E
ILE
12
-14.70
14
E
CYS
3
-13.66
14
E
ILE
12
-12.77
15
E
CYS
3
-12.49
15
E
HIS
11
11.15
15
E
ILE
12
-15.38
1
-11.90
1.20
119.70
107.80
D
D
D
C3'
O3'
P
DA
DA
DC
1
1
2
Y
1
-12.03
1.20
119.70
107.67
D
D
D
C3'
O3'
P
DC
DC
DG
2
2
3
Y
1
-11.84
1.20
119.70
107.86
D
D
D
C3'
O3'
P
DG
DG
DC
3
3
4
Y
1
1.86
0.30
108.30
110.16
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
1
-11.23
1.20
119.70
108.47
D
D
D
C3'
O3'
P
DC
DC
DC
4
4
5
Y
1
2.04
0.30
108.30
110.34
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
2
-11.90
1.20
119.70
107.80
D
D
D
C3'
O3'
P
DA
DA
DC
1
1
2
Y
2
-12.00
1.20
119.70
107.70
D
D
D
C3'
O3'
P
DC
DC
DG
2
2
3
Y
2
-11.89
1.20
119.70
107.81
D
D
D
C3'
O3'
P
DG
DG
DC
3
3
4
Y
2
1.87
0.30
108.30
110.17
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
2
-11.29
1.20
119.70
108.41
D
D
D
C3'
O3'
P
DC
DC
DC
4
4
5
Y
2
2.01
0.30
108.30
110.31
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
3
-11.91
1.20
119.70
107.79
D
D
D
C3'
O3'
P
DA
DA
DC
1
1
2
Y
3
-11.99
1.20
119.70
107.71
D
D
D
C3'
O3'
P
DC
DC
DG
2
2
3
Y
3
-11.91
1.20
119.70
107.79
D
D
D
C3'
O3'
P
DG
DG
DC
3
3
4
Y
3
1.89
0.30
108.30
110.19
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
3
-11.22
1.20
119.70
108.48
D
D
D
C3'
O3'
P
DC
DC
DC
4
4
5
Y
3
2.06
0.30
108.30
110.36
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
4
-11.91
1.20
119.70
107.79
D
D
D
C3'
O3'
P
DA
DA
DC
1
1
2
Y
4
-12.04
1.20
119.70
107.66
D
D
D
C3'
O3'
P
DC
DC
DG
2
2
3
Y
4
-11.88
1.20
119.70
107.82
D
D
D
C3'
O3'
P
DG
DG
DC
3
3
4
Y
4
1.88
0.30
108.30
110.18
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
4
-11.24
1.20
119.70
108.46
D
D
D
C3'
O3'
P
DC
DC
DC
4
4
5
Y
4
2.02
0.30
108.30
110.32
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
5
-11.91
1.20
119.70
107.79
D
D
D
C3'
O3'
P
DA
DA
DC
1
1
2
Y
5
-12.03
1.20
119.70
107.67
D
D
D
C3'
O3'
P
DC
DC
DG
2
2
3
Y
5
-11.88
1.20
119.70
107.82
D
D
D
C3'
O3'
P
DG
DG
DC
3
3
4
Y
5
1.89
0.30
108.30
110.19
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
5
-11.21
1.20
119.70
108.49
D
D
D
C3'
O3'
P
DC
DC
DC
4
4
5
Y
5
2.05
0.30
108.30
110.35
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
6
-11.92
1.20
119.70
107.78
D
D
D
C3'
O3'
P
DA
DA
DC
1
1
2
Y
6
-12.06
1.20
119.70
107.64
D
D
D
C3'
O3'
P
DC
DC
DG
2
2
3
Y
6
-11.93
1.20
119.70
107.77
D
D
D
C3'
O3'
P
DG
DG
DC
3
3
4
Y
6
1.85
0.30
108.30
110.15
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
6
-11.23
1.20
119.70
108.47
D
D
D
C3'
O3'
P
DC
DC
DC
4
4
5
Y
6
2.06
0.30
108.30
110.36
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
7
-11.89
1.20
119.70
107.81
D
D
D
C3'
O3'
P
DA
DA
DC
1
1
2
Y
7
-12.00
1.20
119.70
107.70
D
D
D
C3'
O3'
P
DC
DC
DG
2
2
3
Y
7
-11.89
1.20
119.70
107.81
D
D
D
C3'
O3'
P
DG
DG
DC
3
3
4
Y
7
1.88
0.30
108.30
110.18
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
7
-11.23
1.20
119.70
108.47
D
D
D
C3'
O3'
P
DC
DC
DC
4
4
5
Y
7
2.07
0.30
108.30
110.37
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
8
-11.89
1.20
119.70
107.81
D
D
D
C3'
O3'
P
DA
DA
DC
1
1
2
Y
8
-12.01
1.20
119.70
107.69
D
D
D
C3'
O3'
P
DC
DC
DG
2
2
3
Y
8
-11.91
1.20
119.70
107.79
D
D
D
C3'
O3'
P
DG
DG
DC
3
3
4
Y
8
1.90
0.30
108.30
110.20
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
8
-11.25
1.20
119.70
108.45
D
D
D
C3'
O3'
P
DC
DC
DC
4
4
5
Y
8
2.01
0.30
108.30
110.31
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
9
-11.92
1.20
119.70
107.78
D
D
D
C3'
O3'
P
DA
DA
DC
1
1
2
Y
9
-12.04
1.20
119.70
107.66
D
D
D
C3'
O3'
P
DC
DC
DG
2
2
3
Y
9
-11.86
1.20
119.70
107.84
D
D
D
C3'
O3'
P
DG
DG
DC
3
3
4
Y
9
1.91
0.30
108.30
110.21
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
9
-11.20
1.20
119.70
108.50
D
D
D
C3'
O3'
P
DC
DC
DC
4
4
5
Y
9
2.04
0.30
108.30
110.34
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
10
-11.88
1.20
119.70
107.82
D
D
D
C3'
O3'
P
DA
DA
DC
1
1
2
Y
10
-12.00
1.20
119.70
107.70
D
D
D
C3'
O3'
P
DC
DC
DG
2
2
3
Y
10
-11.84
1.20
119.70
107.86
D
D
D
C3'
O3'
P
DG
DG
DC
3
3
4
Y
10
1.88
0.30
108.30
110.18
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
10
-11.22
1.20
119.70
108.48
D
D
D
C3'
O3'
P
DC
DC
DC
4
4
5
Y
10
2.02
0.30
108.30
110.32
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
11
-11.90
1.20
119.70
107.80
D
D
D
C3'
O3'
P
DA
DA
DC
1
1
2
Y
11
-11.97
1.20
119.70
107.73
D
D
D
C3'
O3'
P
DC
DC
DG
2
2
3
Y
11
-11.88
1.20
119.70
107.82
D
D
D
C3'
O3'
P
DG
DG
DC
3
3
4
Y
11
1.85
0.30
108.30
110.15
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
11
-11.26
1.20
119.70
108.44
D
D
D
C3'
O3'
P
DC
DC
DC
4
4
5
Y
11
2.05
0.30
108.30
110.35
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
12
-11.92
1.20
119.70
107.78
D
D
D
C3'
O3'
P
DA
DA
DC
1
1
2
Y
12
-12.00
1.20
119.70
107.70
D
D
D
C3'
O3'
P
DC
DC
DG
2
2
3
Y
12
-11.89
1.20
119.70
107.81
D
D
D
C3'
O3'
P
DG
DG
DC
3
3
4
Y
12
1.86
0.30
108.30
110.16
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
12
-11.21
1.20
119.70
108.49
D
D
D
C3'
O3'
P
DC
DC
DC
4
4
5
Y
12
2.00
0.30
108.30
110.30
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
13
-11.94
1.20
119.70
107.76
D
D
D
C3'
O3'
P
DA
DA
DC
1
1
2
Y
13
-12.01
1.20
119.70
107.69
D
D
D
C3'
O3'
P
DC
DC
DG
2
2
3
Y
13
-11.91
1.20
119.70
107.79
D
D
D
C3'
O3'
P
DG
DG
DC
3
3
4
Y
13
1.91
0.30
108.30
110.21
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
13
-11.27
1.20
119.70
108.43
D
D
D
C3'
O3'
P
DC
DC
DC
4
4
5
Y
13
1.99
0.30
108.30
110.29
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
13
-4.36
0.70
120.80
116.44
E
E
E
CB
CG
CD2
PHE
PHE
PHE
4
4
4
N
14
-11.89
1.20
119.70
107.81
D
D
D
C3'
O3'
P
DA
DA
DC
1
1
2
Y
14
-11.98
1.20
119.70
107.72
D
D
D
C3'
O3'
P
DC
DC
DG
2
2
3
Y
14
-11.89
1.20
119.70
107.81
D
D
D
C3'
O3'
P
DG
DG
DC
3
3
4
Y
14
1.84
0.30
108.30
110.14
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
14
-11.23
1.20
119.70
108.47
D
D
D
C3'
O3'
P
DC
DC
DC
4
4
5
Y
14
2.05
0.30
108.30
110.35
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
15
-11.92
1.20
119.70
107.78
D
D
D
C3'
O3'
P
DA
DA
DC
1
1
2
Y
15
-12.02
1.20
119.70
107.68
D
D
D
C3'
O3'
P
DC
DC
DG
2
2
3
Y
15
-11.88
1.20
119.70
107.82
D
D
D
C3'
O3'
P
DG
DG
DC
3
3
4
Y
15
1.88
0.30
108.30
110.18
D
D
D
O4'
C1'
N1
DC
DC
DC
4
4
4
N
15
-11.24
1.20
119.70
108.46
D
D
D
C3'
O3'
P
DC
DC
DC
4
4
5
Y
15
2.03
0.30
108.30
110.33
D
D
D
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
D
D
P
OP3
DA
DA
1
1
-0.124
0.012
1.607
1.483
N
2
D
D
P
OP3
DA
DA
1
1
-0.124
0.012
1.607
1.483
N
3
D
D
P
OP3
DA
DA
1
1
-0.123
0.012
1.607
1.484
N
4
D
D
P
OP3
DA
DA
1
1
-0.123
0.012
1.607
1.484
N
5
D
D
P
OP3
DA
DA
1
1
-0.122
0.012
1.607
1.485
N
6
D
D
P
OP3
DA
DA
1
1
-0.123
0.012
1.607
1.484
N
7
D
D
P
OP3
DA
DA
1
1
-0.123
0.012
1.607
1.484
N
8
D
D
P
OP3
DA
DA
1
1
-0.123
0.012
1.607
1.484
N
9
D
D
P
OP3
DA
DA
1
1
-0.123
0.012
1.607
1.484
N
10
D
D
P
OP3
DA
DA
1
1
-0.123
0.012
1.607
1.484
N
11
D
D
P
OP3
DA
DA
1
1
-0.124
0.012
1.607
1.483
N
12
D
D
P
OP3
DA
DA
1
1
-0.123
0.012
1.607
1.484
N
13
D
D
P
OP3
DA
DA
1
1
-0.124
0.012
1.607
1.483
N
14
D
D
P
OP3
DA
DA
1
1
-0.122
0.012
1.607
1.485
N
15
D
D
P
OP3
DA
DA
1
1
-0.123
0.012
1.607
1.484
N
1
E
CYS
16
-65.21
-147.94
1
E
ARG
17
177.65
-38.36
2
E
CYS
16
-78.86
-117.70
2
E
ARG
17
170.71
-73.09
3
E
ARG
17
-159.41
29.48
4
E
ARG
14
-59.89
-8.73
7
E
CYS
16
-72.58
-72.00
7
E
ARG
17
78.30
-54.86
10
E
ARG
14
-59.99
-8.19
12
E
ARG
14
-59.61
-9.37
13
E
ARG
14
-59.68
-8.27
14
E
ARG
17
-145.75
28.26
15
E
ARG
17
-148.06
28.40
ZINC-AND SEQUENCE-DEPENDENT BINDING TO NUCLEIC ACIDS BY THE N-TERMINAL ZINC FINGER DOMAIN OF THE HIV-1 NUCLEOCAPSID PROTEIN: NMR STRUCTURE OF THE COMPLEX WITH THE PSI-SITE ANALOG, D/ACGCC
1
N
N
2
N
N
3
N
N
E
ILE
12
B
ILE
12
HELX_P
E
CYS
16
B
CYS
16
5
1
5
metalc
2.313
E
CYS
3
B
SG
CYS
3
1_555
E
ZN
19
C
ZN
ZN
1_555
metalc
2.302
E
CYS
6
B
SG
CYS
6
1_555
E
ZN
19
C
ZN
ZN
1_555
metalc
2.018
E
HIS
11
B
NE2
HIS
11
1_555
E
ZN
19
C
ZN
ZN
1_555
metalc
2.301
E
CYS
16
B
SG
CYS
16
1_555
E
ZN
19
C
ZN
ZN
1_555
Viral protein/DNA
Viral protein/DNA, Viral protein-DNA complex
GAG_HV1LW
UNP
2
389
Q70622
1HVN
PDB
1
1HVN
389
406
1HVN
1
18
Q70622
E
1
1
18
1
5
1HVN
1
5
1HVN
D
2
1
5
BINDING SITE FOR RESIDUE ZN E 19
E
ZN
19
Software
4
E
CYS
3
B
CYS
3
4
1_555
E
CYS
6
B
CYS
6
4
1_555
E
HIS
11
B
HIS
11
4
1_555
E
CYS
16
B
CYS
16
4
1_555
1
P 1