0.011743
0.000000
0.000000
0.000000
0.011743
0.000000
0.000000
0.000000
0.011743
0.00000
0.00000
0.00000
Arold, S.
Franken, P.
Dumas, C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
90.00
85.160
85.160
85.160
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
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 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
C9 H11 N O2
165.189
y
PHENYLALANINE
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
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
UK
Structure
STRUE6
2005
0969-2126
5
1361
1372
10.1016/S0969-2126(97)00286-4
9351809
The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling.
1997
US
Cell(Cambridge,Mass.)
CELLB5
0998
0092-8674
85
931
Crystal Structure of the Conserved Core of HIV-1 Nef Complexed with a Src Family SH3 Domain
1996
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
3
340
The Solution Structure of HIV-1 Nef Reveals an Unexpected Fold and Permits Delineation of the Binding Surface for the SH3 Domain of HCK Tyrosine Protein Kinase
1996
10.2210/pdb1avv/pdb
pdb_00001avv
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
TWO BENT MIRRORS
CCD
1996-10-04
PRINCETON 2K
SI(111)
M
x-ray
1
1.0373
1.0
BM02
ESRF
1.0373
SYNCHROTRON
ESRF BEAMLINE BM02
17568.723
NEGATIVE FACTOR
CORE DOMAIN
DEL(2-57), N-TERMINAL RESIDUES GS (PART OF A THROMBIN CLEAVAGE SITE)
1
man
polymer
NEF, F-PROTEIN
no
no
GSLEAQEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRY
PLTFGWCYKLVPVEPDKVEEANKGENTSLLHPVSLHGMDDPEREVLEWRFDSRLAFHHVARELHPEYFKNC
GSLEAQEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRY
PLTFGWCYKLVPVEPDKVEEANKGENTSLLHPVSLHGMDDPEREVLEWRFDSRLAFHHVARELHPEYFKNC
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
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
Lentivirus
Escherichia
Escherichia coli
sample
BL21
HIV-1 NEF
11676
Human immunodeficiency virus 1
ISOLATE LAI
HIV-1 NEF
469008
Escherichia coli BL21(DE3)
BL21 (DE3)
PGEX-2T
1
3.1
61.
7.5
pH 7.5
diffrn_source
diffrn_source
database_2
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Data collection
Data collection
Database references
Refinement description
1
0
1998-03-25
1
1
2008-03-24
1
2
2011-07-13
1
3
2018-04-04
1
4
2018-04-11
1
5
2023-08-02
_diffrn_source.type
_diffrn_source.pdbx_synchrotron_beamline
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
Y
BNL
1997-09-21
REL
1EFN
PDB ENTRY 1EFN
PDB
experimental model
n
1
56
A
n
2
57
A
n
3
58
A
n
4
59
A
n
5
60
A
n
6
61
A
n
7
62
A
n
8
63
A
n
9
64
A
n
10
65
A
n
11
66
A
n
12
67
A
n
13
68
A
n
14
69
A
n
15
70
A
n
16
71
A
n
17
72
A
n
18
73
A
VAL
74
n
19
VAL
74
A
PRO
75
n
20
PRO
75
A
LEU
76
n
21
LEU
76
A
ARG
77
n
22
ARG
77
A
PRO
78
n
23
PRO
78
A
MET
79
n
24
MET
79
A
THR
80
n
25
THR
80
A
TYR
81
n
26
TYR
81
A
LYS
82
n
27
LYS
82
A
ALA
83
n
28
ALA
83
A
ALA
84
n
29
ALA
84
A
VAL
85
n
30
VAL
85
A
ASP
86
n
31
ASP
86
A
LEU
87
n
32
LEU
87
A
SER
88
n
33
SER
88
A
HIS
89
n
34
HIS
89
A
PHE
90
n
35
PHE
90
A
LEU
91
n
36
LEU
91
A
LYS
92
n
37
LYS
92
A
GLU
93
n
38
GLU
93
A
LYS
94
n
39
LYS
94
A
GLY
95
n
40
GLY
95
A
GLY
96
n
41
GLY
96
A
LEU
97
n
42
LEU
97
A
GLU
98
n
43
GLU
98
A
GLY
99
n
44
GLY
99
A
LEU
100
n
45
LEU
100
A
ILE
101
n
46
ILE
101
A
HIS
102
n
47
HIS
102
A
SER
103
n
48
SER
103
A
GLN
104
n
49
GLN
104
A
ARG
105
n
50
ARG
105
A
ARG
106
n
51
ARG
106
A
GLN
107
n
52
GLN
107
A
ASP
108
n
53
ASP
108
A
ILE
109
n
54
ILE
109
A
LEU
110
n
55
LEU
110
A
ASP
111
n
56
ASP
111
A
LEU
112
n
57
LEU
112
A
TRP
113
n
58
TRP
113
A
ILE
114
n
59
ILE
114
A
TYR
115
n
60
TYR
115
A
HIS
116
n
61
HIS
116
A
THR
117
n
62
THR
117
A
GLN
118
n
63
GLN
118
A
GLY
119
n
64
GLY
119
A
TYR
120
n
65
TYR
120
A
PHE
121
n
66
PHE
121
A
PRO
122
n
67
PRO
122
A
ASP
123
n
68
ASP
123
A
TRP
124
n
69
TRP
124
A
GLN
125
n
70
GLN
125
A
ASN
126
n
71
ASN
126
A
TYR
127
n
72
TYR
127
A
THR
128
n
73
THR
128
A
PRO
129
n
74
PRO
129
A
GLY
130
n
75
GLY
130
A
PRO
131
n
76
PRO
131
A
GLY
132
n
77
GLY
132
A
VAL
133
n
78
VAL
133
A
ARG
134
n
79
ARG
134
A
TYR
135
n
80
TYR
135
A
PRO
136
n
81
PRO
136
A
LEU
137
n
82
LEU
137
A
THR
138
n
83
THR
138
A
PHE
139
n
84
PHE
139
A
GLY
140
n
85
GLY
140
A
TRP
141
n
86
TRP
141
A
CYS
142
n
87
CYS
142
A
TYR
143
n
88
TYR
143
A
LYS
144
n
89
LYS
144
A
LEU
145
n
90
LEU
145
A
VAL
146
n
91
VAL
146
A
PRO
147
n
92
PRO
147
A
n
93
148
A
n
94
149
A
n
95
150
A
n
96
151
A
n
97
152
A
n
98
153
A
n
99
154
A
n
100
155
A
n
101
156
A
n
102
157
A
n
103
158
A
n
104
159
A
n
105
160
A
n
106
161
A
n
107
162
A
n
108
163
A
n
109
164
A
n
110
165
A
n
111
166
A
n
112
167
A
n
113
168
A
n
114
169
A
n
115
170
A
n
116
171
A
n
117
172
A
n
118
173
A
n
119
174
A
n
120
175
A
n
121
176
A
n
122
177
A
n
123
178
A
GLU
179
n
124
GLU
179
A
VAL
180
n
125
VAL
180
A
LEU
181
n
126
LEU
181
A
GLU
182
n
127
GLU
182
A
TRP
183
n
128
TRP
183
A
ARG
184
n
129
ARG
184
A
PHE
185
n
130
PHE
185
A
ASP
186
n
131
ASP
186
A
SER
187
n
132
SER
187
A
ARG
188
n
133
ARG
188
A
LEU
189
n
134
LEU
189
A
ALA
190
n
135
ALA
190
A
PHE
191
n
136
PHE
191
A
HIS
192
n
137
HIS
192
A
HIS
193
n
138
HIS
193
A
VAL
194
n
139
VAL
194
A
ALA
195
n
140
ALA
195
A
ARG
196
n
141
ARG
196
A
GLU
197
n
142
GLU
197
A
LEU
198
n
143
LEU
198
A
HIS
199
n
144
HIS
199
A
PRO
200
n
145
PRO
200
A
GLU
201
n
146
GLU
201
A
TYR
202
n
147
TYR
202
A
PHE
203
n
148
PHE
203
A
n
149
204
A
n
150
205
A
n
151
206
A
author_defined_assembly
2
dimeric
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
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_567
x,-y+1,-z+2
crystal symmetry operation
0.0000000000
85.1600000000
170.3200000000
A
O
LYS
144
A
O
LYS
89
A
N
ARG
184
A
N
ARG
129
1
A
GLY
56
A
GLY
1
1
Y
1
A
SER
57
A
SER
2
1
Y
1
A
LEU
58
A
LEU
3
1
Y
1
A
GLU
59
A
GLU
4
1
Y
1
A
ALA
60
A
ALA
5
1
Y
1
A
GLN
61
A
GLN
6
1
Y
1
A
GLU
62
A
GLU
7
1
Y
1
A
GLU
63
A
GLU
8
1
Y
1
A
GLU
64
A
GLU
9
1
Y
1
A
GLU
65
A
GLU
10
1
Y
1
A
VAL
66
A
VAL
11
1
Y
1
A
GLY
67
A
GLY
12
1
Y
1
A
PHE
68
A
PHE
13
1
Y
1
A
PRO
69
A
PRO
14
1
Y
1
A
VAL
70
A
VAL
15
1
Y
1
A
THR
71
A
THR
16
1
Y
1
A
PRO
72
A
PRO
17
1
Y
1
A
GLN
73
A
GLN
18
1
Y
1
A
VAL
148
A
VAL
93
1
Y
1
A
GLU
149
A
GLU
94
1
Y
1
A
PRO
150
A
PRO
95
1
Y
1
A
ASP
151
A
ASP
96
1
Y
1
A
LYS
152
A
LYS
97
1
Y
1
A
VAL
153
A
VAL
98
1
Y
1
A
GLU
154
A
GLU
99
1
Y
1
A
GLU
155
A
GLU
100
1
Y
1
A
ALA
156
A
ALA
101
1
Y
1
A
ASN
157
A
ASN
102
1
Y
1
A
LYS
158
A
LYS
103
1
Y
1
A
GLY
159
A
GLY
104
1
Y
1
A
GLU
160
A
GLU
105
1
Y
1
A
ASN
161
A
ASN
106
1
Y
1
A
THR
162
A
THR
107
1
Y
1
A
SER
163
A
SER
108
1
Y
1
A
LEU
164
A
LEU
109
1
Y
1
A
LEU
165
A
LEU
110
1
Y
1
A
HIS
166
A
HIS
111
1
Y
1
A
PRO
167
A
PRO
112
1
Y
1
A
VAL
168
A
VAL
113
1
Y
1
A
SER
169
A
SER
114
1
Y
1
A
LEU
170
A
LEU
115
1
Y
1
A
HIS
171
A
HIS
116
1
Y
1
A
GLY
172
A
GLY
117
1
Y
1
A
MET
173
A
MET
118
1
Y
1
A
ASP
174
A
ASP
119
1
Y
1
A
ASP
175
A
ASP
120
1
Y
1
A
PRO
176
A
PRO
121
1
Y
1
A
GLU
177
A
GLU
122
1
Y
1
A
ARG
178
A
ARG
123
1
Y
1
A
LYS
204
A
LYS
149
1
Y
1
A
ASN
205
A
ASN
150
1
Y
1
A
CYS
206
A
CYS
151
1
Y
1
10.52
1.50
119.30
129.82
A
A
A
C
N
CA
PHE
PRO
PRO
121
122
122
Y
1
A
PRO
75
-36.85
123.09
1
A
LEU
76
-54.34
101.83
1
A
LYS
94
-155.44
52.54
1
A
LEU
100
-30.95
120.33
1
A
THR
117
-55.58
-76.91
1
A
PRO
122
-61.49
65.43
1
A
ASP
123
-150.53
17.22
1
A
CYS
142
-106.25
70.64
1
A
ASP
186
179.62
111.30
1
A
HIS
199
-107.84
78.51
38.
0.2800000
0.2200000
0.2200000
3.0
30.
3139
7.4
78.8
RANDOM
10000000.00
0.001
1
2.0
MOLECULAR REPLACEMENT AND MIRAS
PDB ENTRY 1EFN
3.0
30.
0
895
0
0
895
0.009
1.9
23.7
1.1
3.0
25.0
1AVV
3812
-3.0
0.0720000
1
9.
4.9
93.
phasing
AMoRE
refinement
X-PLOR
3.8
data reduction
XDS
data scaling
XSCALE
HIV-1 NEF PROTEIN, UNLIGANDED CORE DOMAIN
1
N
N
A
TYR
81
A
TYR
26
HELX_P
A
GLU
93
A
GLU
38
1
1
13
A
GLN
104
A
GLN
49
HELX_P
A
GLN
118
A
GLN
63
1
2
15
A
SER
187
A
SER
132
HELX_P
A
ALA
190
A
ALA
135
5
3
4
A
VAL
194
A
VAL
139
HELX_P
A
LEU
198
A
LEU
143
1
4
5
MYRISTYLATION
MYRISTYLATION, GTP-BINDING, PHOSPHORYLATION, HIV-1, NEF, VIRUS, PXXP MOTIF
A
GLY
130
A
GLY
75
1
A
PRO
131
A
PRO
76
0.29
NEF_HV1BR
UNP
1
1
P03406
MGGKWSKSSVVGWPTVRERMRRAEPAADGVGAASRDLEKHGAITSSNTAATNAACAWLEAQEEEEVGFPVTPQVPLRPMT
YKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGE
NTSLLHPVSLHGMDDPEREVLEWRFDSRLAFHHVARELHPEYFKNC
58
206
1AVV
58
206
P03406
A
1
3
151
2
anti-parallel
A
TYR
143
A
TYR
88
A
VAL
146
A
VAL
91
A
GLU
182
A
GLU
127
A
PHE
185
A
PHE
130
195
P 2 3