1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Kodera, Y.
Sato, K.
Tsukahara, T.
Komatsu, H.
Maeda, T.
Kohno, T.
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
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 H15 N2 O2 1
147.195
y
LYSINE
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
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
US
Biochemistry
BICHAW
0033
0006-2960
37
17704
17713
10.1021/bi981818o
9922136
High-resolution solution NMR structure of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein.
1998
10.2210/pdb1nc8/pdb
pdb_00001nc8
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3389.924
NUCLEOCAPSID PROTEIN
RESIDUES 1-29
1
man
polymer
65.409
ZINC ION
1
syn
non-polymer
no
no
AQQRKVIRCWNCGKEGHSARQCRAPRRQG
AQQRKVIRCWNCGKEGHSARQCRAPRRQG
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
Lentivirus
sample
11709
Human immunodeficiency virus 2
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1999-05-25
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
_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
1998-05-14
REL
ZN
ZINC ION
100
15
NOESY
COSY
TOCSY
5.8
288
K
simulated annealing
BRUNGER
refinement
X-PLOR
3.1
structure solution
X-PLOR
3.1
500
Bruker
DMX500
ZN
30
2
ZN
ZN
30
A
ALA
1
n
1
ALA
1
A
GLN
2
n
2
GLN
2
A
GLN
3
n
3
GLN
3
A
ARG
4
n
4
ARG
4
A
LYS
5
n
5
LYS
5
A
VAL
6
n
6
VAL
6
A
ILE
7
n
7
ILE
7
A
ARG
8
n
8
ARG
8
A
CYS
9
n
9
CYS
9
A
TRP
10
n
10
TRP
10
A
ASN
11
n
11
ASN
11
A
CYS
12
n
12
CYS
12
A
GLY
13
n
13
GLY
13
A
LYS
14
n
14
LYS
14
A
GLU
15
n
15
GLU
15
A
GLY
16
n
16
GLY
16
A
HIS
17
n
17
HIS
17
A
SER
18
n
18
SER
18
A
ALA
19
n
19
ALA
19
A
ARG
20
n
20
ARG
20
A
GLN
21
n
21
GLN
21
A
CYS
22
n
22
CYS
22
A
ARG
23
n
23
ARG
23
A
ALA
24
n
24
ALA
24
A
PRO
25
n
25
PRO
25
A
ARG
26
n
26
ARG
26
A
ARG
27
n
27
ARG
27
A
GLN
28
n
28
GLN
28
A
GLY
29
n
29
GLY
29
A
author_defined_assembly
1
monomeric
A
CYS
9
A
SG
CYS
9
1_555
A
ZN
30
B
ZN
ZN
1_555
A
CYS
12
A
SG
CYS
12
1_555
86.9
A
CYS
9
A
SG
CYS
9
1_555
A
ZN
30
B
ZN
ZN
1_555
A
HIS
17
A
CE1
HIS
17
1_555
96.3
A
CYS
12
A
SG
CYS
12
1_555
A
ZN
30
B
ZN
ZN
1_555
A
HIS
17
A
CE1
HIS
17
1_555
174.7
A
CYS
9
A
SG
CYS
9
1_555
A
ZN
30
B
ZN
ZN
1_555
A
HIS
17
A
NE2
HIS
17
1_555
69.3
A
CYS
12
A
SG
CYS
12
1_555
A
ZN
30
B
ZN
ZN
1_555
A
HIS
17
A
NE2
HIS
17
1_555
144.0
A
HIS
17
A
CE1
HIS
17
1_555
A
ZN
30
B
ZN
ZN
1_555
A
HIS
17
A
NE2
HIS
17
1_555
41.3
A
CYS
9
A
SG
CYS
9
1_555
A
ZN
30
B
ZN
ZN
1_555
A
CYS
22
A
SG
CYS
22
1_555
68.4
A
CYS
12
A
SG
CYS
12
1_555
A
ZN
30
B
ZN
ZN
1_555
A
CYS
22
A
SG
CYS
22
1_555
91.2
A
HIS
17
A
CE1
HIS
17
1_555
A
ZN
30
B
ZN
ZN
1_555
A
CYS
22
A
SG
CYS
22
1_555
93.9
A
HIS
17
A
NE2
HIS
17
1_555
A
ZN
30
B
ZN
ZN
1_555
A
CYS
22
A
SG
CYS
22
1_555
55.5
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
1
A
A
HE1
ZN
HIS
ZN
17
30
1.20
1
A
A
NE2
SG
HIS
CYS
17
22
2.02
5
A
A
HB2
ZN
LYS
ZN
14
30
1.55
5
A
A
NE2
SG
HIS
CYS
17
22
2.05
6
A
A
HE1
ZN
HIS
ZN
17
30
1.20
6
A
A
NE2
SG
HIS
CYS
17
22
2.10
6
A
A
SG
NE2
CYS
HIS
9
17
2.18
7
A
A
HE1
ZN
HIS
ZN
17
30
1.54
8
A
A
HE1
ZN
HIS
ZN
17
30
1.54
8
A
A
NE2
SG
HIS
CYS
17
22
2.15
10
A
A
HE1
ZN
HIS
ZN
17
30
1.14
10
A
A
NE2
SG
HIS
CYS
17
22
2.16
11
A
A
HE1
ZN
HIS
ZN
17
30
1.07
11
A
A
NE2
SG
HIS
CYS
17
22
2.08
12
A
A
HE1
ZN
HIS
ZN
17
30
1.21
13
A
A
HE1
ZN
HIS
ZN
17
30
1.10
13
A
A
NE2
SG
HIS
CYS
17
22
2.08
14
A
A
NE2
SG
HIS
CYS
17
22
2.14
15
A
A
NE2
SG
HIS
CYS
17
22
2.04
1
A
ARG
4
0.317
SIDE CHAIN
1
A
ARG
8
0.267
SIDE CHAIN
1
A
ARG
20
0.285
SIDE CHAIN
1
A
ARG
23
0.183
SIDE CHAIN
1
A
ARG
26
0.306
SIDE CHAIN
1
A
ARG
27
0.313
SIDE CHAIN
2
A
ARG
4
0.230
SIDE CHAIN
2
A
ARG
8
0.311
SIDE CHAIN
2
A
ARG
20
0.197
SIDE CHAIN
2
A
ARG
23
0.214
SIDE CHAIN
2
A
ARG
26
0.311
SIDE CHAIN
2
A
ARG
27
0.180
SIDE CHAIN
3
A
ARG
8
0.270
SIDE CHAIN
3
A
ARG
20
0.181
SIDE CHAIN
3
A
ARG
26
0.277
SIDE CHAIN
3
A
ARG
27
0.247
SIDE CHAIN
4
A
ARG
4
0.202
SIDE CHAIN
4
A
ARG
8
0.271
SIDE CHAIN
4
A
ARG
20
0.202
SIDE CHAIN
4
A
ARG
26
0.317
SIDE CHAIN
4
A
ARG
27
0.150
SIDE CHAIN
5
A
ARG
8
0.284
SIDE CHAIN
5
A
ARG
20
0.294
SIDE CHAIN
5
A
ARG
23
0.239
SIDE CHAIN
5
A
ARG
27
0.089
SIDE CHAIN
6
A
ARG
4
0.250
SIDE CHAIN
6
A
ARG
8
0.310
SIDE CHAIN
6
A
ARG
20
0.180
SIDE CHAIN
6
A
ARG
23
0.269
SIDE CHAIN
6
A
ARG
27
0.217
SIDE CHAIN
7
A
ARG
4
0.202
SIDE CHAIN
7
A
ARG
8
0.293
SIDE CHAIN
7
A
ARG
20
0.207
SIDE CHAIN
7
A
ARG
23
0.310
SIDE CHAIN
7
A
ARG
26
0.106
SIDE CHAIN
7
A
ARG
27
0.222
SIDE CHAIN
8
A
ARG
4
0.108
SIDE CHAIN
8
A
ARG
8
0.211
SIDE CHAIN
8
A
ARG
20
0.222
SIDE CHAIN
8
A
ARG
23
0.273
SIDE CHAIN
8
A
ARG
27
0.315
SIDE CHAIN
9
A
ARG
4
0.300
SIDE CHAIN
9
A
ARG
8
0.231
SIDE CHAIN
9
A
ARG
20
0.224
SIDE CHAIN
9
A
ARG
23
0.317
SIDE CHAIN
9
A
ARG
26
0.124
SIDE CHAIN
9
A
ARG
27
0.318
SIDE CHAIN
10
A
ARG
4
0.272
SIDE CHAIN
10
A
ARG
8
0.317
SIDE CHAIN
10
A
ARG
20
0.299
SIDE CHAIN
10
A
ARG
23
0.288
SIDE CHAIN
10
A
ARG
26
0.306
SIDE CHAIN
10
A
ARG
27
0.185
SIDE CHAIN
11
A
ARG
4
0.264
SIDE CHAIN
11
A
ARG
8
0.211
SIDE CHAIN
11
A
ARG
23
0.315
SIDE CHAIN
11
A
ARG
26
0.303
SIDE CHAIN
11
A
ARG
27
0.215
SIDE CHAIN
12
A
ARG
4
0.278
SIDE CHAIN
12
A
ARG
8
0.280
SIDE CHAIN
12
A
ARG
20
0.274
SIDE CHAIN
12
A
ARG
23
0.262
SIDE CHAIN
12
A
ARG
26
0.248
SIDE CHAIN
12
A
ARG
27
0.274
SIDE CHAIN
13
A
ARG
4
0.316
SIDE CHAIN
13
A
ARG
8
0.207
SIDE CHAIN
13
A
ARG
20
0.265
SIDE CHAIN
13
A
ARG
23
0.240
SIDE CHAIN
13
A
ARG
26
0.258
SIDE CHAIN
13
A
ARG
27
0.198
SIDE CHAIN
14
A
ARG
8
0.258
SIDE CHAIN
14
A
ARG
20
0.308
SIDE CHAIN
14
A
ARG
23
0.199
SIDE CHAIN
14
A
ARG
26
0.307
SIDE CHAIN
14
A
ARG
27
0.087
SIDE CHAIN
15
A
ARG
4
0.300
SIDE CHAIN
15
A
ARG
8
0.310
SIDE CHAIN
15
A
ARG
20
0.110
SIDE CHAIN
15
A
ARG
23
0.237
SIDE CHAIN
15
A
ARG
26
0.105
SIDE CHAIN
15
A
ARG
27
0.262
SIDE CHAIN
1
A
GLN
3
44.62
76.23
1
A
ASN
11
-41.00
-76.93
1
A
ALA
24
-74.86
-74.72
1
A
ARG
27
-178.79
85.69
2
A
ARG
4
177.21
76.50
2
A
CYS
9
-41.78
109.63
2
A
ASN
11
-38.91
-79.29
2
A
ALA
24
-81.00
-72.86
2
A
ARG
27
174.81
105.88
3
A
LYS
5
-96.08
-96.77
3
A
VAL
6
49.02
176.86
3
A
CYS
9
-41.05
98.88
3
A
ASN
11
-39.79
-79.12
3
A
ALA
24
-71.57
-77.20
3
A
ARG
27
166.61
100.02
4
A
GLN
2
-71.91
-140.92
4
A
CYS
9
-48.43
97.30
4
A
ALA
24
-87.37
-76.50
4
A
ARG
27
169.46
95.45
4
A
GLN
28
59.91
15.89
5
A
GLN
3
65.32
72.21
5
A
ARG
4
-163.43
85.88
5
A
CYS
9
-43.00
108.32
5
A
ALA
24
-72.96
-82.08
5
A
ARG
27
164.17
95.93
6
A
LYS
5
55.09
96.61
6
A
CYS
9
-45.77
98.90
6
A
ALA
24
-72.02
-77.91
6
A
ARG
27
171.14
103.80
7
A
GLN
2
-113.57
61.57
7
A
LYS
5
-142.19
-43.20
7
A
CYS
9
-39.91
93.89
7
A
ALA
24
-68.12
-80.05
7
A
ARG
27
172.21
113.55
8
A
GLN
2
176.39
151.67
8
A
LYS
5
168.23
143.09
8
A
VAL
6
-43.07
155.42
8
A
CYS
9
-43.22
101.55
8
A
ALA
24
-82.16
-80.82
8
A
ARG
27
172.87
100.92
9
A
VAL
6
54.49
166.83
9
A
ALA
24
-68.65
-93.91
9
A
ARG
27
175.62
103.14
10
A
CYS
9
-34.50
97.96
10
A
ALA
24
-65.37
-78.52
10
A
ARG
27
178.31
111.44
11
A
ARG
4
64.92
159.03
11
A
GLU
15
-32.20
137.13
11
A
CYS
22
-54.94
96.65
11
A
ALA
24
-74.42
-76.63
12
A
GLN
2
65.53
-85.48
12
A
GLU
15
-39.23
128.84
12
A
ALA
24
-68.19
-83.22
12
A
ARG
27
170.86
97.19
13
A
GLN
3
67.39
-177.17
13
A
ARG
4
73.55
173.04
13
A
LYS
5
-105.55
78.94
13
A
CYS
9
-41.88
109.59
13
A
ASN
11
-44.72
-70.18
13
A
GLU
15
-36.44
138.36
13
A
ALA
24
-83.54
-73.05
13
A
ARG
27
-179.24
111.63
14
A
GLN
2
-114.27
-158.81
14
A
GLN
3
60.42
149.83
14
A
VAL
6
57.75
118.83
14
A
CYS
9
-43.27
98.80
14
A
ASN
11
-41.66
-77.54
14
A
GLU
15
-29.82
137.03
14
A
ARG
27
-162.11
106.69
15
A
LYS
5
-178.41
36.64
15
A
VAL
6
-43.78
159.09
15
A
GLU
15
-36.49
145.88
15
A
ALA
24
-80.61
-76.15
15
A
ARG
27
-177.23
100.07
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
phasing
X-PLOR
3.1
HIGH-RESOLUTION SOLUTION NMR STRUCTURE OF THE MINIMAL ACTIVE DOMAIN OF THE HUMAN IMMUNODEFICIENCY VIRUS TYPE-2 NUCLEOCAPSID PROTEIN, 15 STRUCTURES
1
Y
N
2
N
N
A
ALA
19
A
ALA
19
HELX_P
A
GLN
21
A
GLN
21
5
1
3
disulf
2.588
A
CYS
9
A
SG
CYS
9
1_555
A
CYS
22
A
SG
CYS
22
1_555
metalc
2.300
A
CYS
9
A
SG
CYS
9
1_555
A
ZN
30
B
ZN
ZN
1_555
metalc
2.296
A
CYS
12
A
SG
CYS
12
1_555
A
ZN
30
B
ZN
ZN
1_555
metalc
1.722
A
HIS
17
A
CE1
HIS
17
1_555
A
ZN
30
B
ZN
ZN
1_555
metalc
1.996
A
HIS
17
A
NE2
HIS
17
1_555
A
ZN
30
B
ZN
ZN
1_555
metalc
2.302
A
CYS
22
A
SG
CYS
22
1_555
A
ZN
30
B
ZN
ZN
1_555
VIRAL PROTEIN
NUCLEOCAPSID PROTEIN, HIV-2, RNA RECOGNITION, ZINC FINGER, Viral protein
POL_HV2G1
UNP
1
1
P18042
MGARNSVLRGKKADELEKIRLRPSGKKKYRLKHIVWAANELDKFGLAESLLESKEGCQKILTVLDPLVPTGSENLKSLFN
TVCVIWCLHAEEKVKDTEEAKKLVQRHLGAETGTAEKMPSTSRPTAPPSGRGRNFPVQQTGGGNYIHVPLSPRTLNAWVK
LVEDKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIREIINDEAADWDAQHPIPGPLPAGQLRDPRGSDIAG
TTSTVEEQIQWMYRPQNPVPVGNIYRRWIQIGLQKCVRMYNPTNILDVKQGPKEPFQSYVDRFYKSLRAEQTDPAVKNWM
TQTLLIQNANPDCKLVLKGLGMNPTLEEMLTACQGVGGPGQKARLMAEALKEALTPPPIPFAAAQQRKVIRCWNCGKEGH
SARQCRAPRRQGCWKCGKTGHVMAKCPERQAGFLGMGPWGKKPRNFPVAQAPPGLIPTAPPADPAVDLLERYMQQGREQR
EQRERPYKEVTEDLLHLEQGKAPHREATEDLLHLNSLFGKDQ
384
412
1NC8
1
29
P18042
A
1
1
29
CCHC ZINC FINGER.
Unknown
14
BINDING SITE FOR RESIDUE ZN A 30
A
ZN
30
Software
5
A
CYS
9
A
CYS
9
14
1_555
A
TRP
10
A
TRP
10
14
1_555
A
ASN
11
A
ASN
11
14
1_555
A
CYS
12
A
CYS
12
14
1_555
A
GLY
13
A
GLY
13
14
1_555
A
LYS
14
A
LYS
14
14
1_555
A
GLU
15
A
GLU
15
14
1_555
A
GLY
16
A
GLY
16
14
1_555
A
HIS
17
A
HIS
17
14
1_555
A
SER
18
A
SER
18
14
1_555
A
ALA
19
A
ALA
19
14
1_555
A
ARG
20
A
ARG
20
14
1_555
A
GLN
21
A
GLN
21
14
1_555
A
CYS
22
A
CYS
22
14
1_555
A
CYS
9
A
CYS
9
5
1_555
A
CYS
12
A
CYS
12
5
1_555
A
LYS
14
A
LYS
14
5
1_555
A
HIS
17
A
HIS
17
5
1_555
A
CYS
22
A
CYS
22
5
1_555
1
P 1