1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Geyer, M.
Kalbitzer, H.R.
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
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
C14 H28 O2
228.371
MYRISTIC ACID
non-polymer
H2 N
16.023
AMINO GROUP
non-polymer
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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
289
123
138
10.1006/jmbi.1999.2740
10339411
Structure of the anchor-domain of myristoylated and non-myristoylated HIV-1 Nef protein.
1999
US
Protein Sci.
PRCIEI
0795
0961-8368
6
1248
1263
10.1002/pro.5560060613
9194185
Refined solution structure and backbone dynamics of HIV-1 Nef.
1997
US
Biochemistry
BICHAW
0033
0006-2960
36
5970
5980
10.1021/bi9629945
9166767
Solution structure of a polypeptide from the N terminus of the HIV protein Nef.
1997
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
942
10.1016/s0092-8674(00)81276-3
8681387
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
345
10.1038/nsb0496-340
8599760
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
IX
Eur.J.Biochem.
EJBCAI
0262
0014-2956
223
589
593
10.1111/j.1432-1033.1994.tb19029.x
8055930
A possible regulation of negative factor (Nef) activity of human immunodeficiency virus type 1 by the viral protease.
1994
10.2210/pdb1qa5/pdb
pdb_00001qa5
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
6027.812
PROTEIN (MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN (MYRISTATE-GLY2 TO TRP57))
1
syn
polymer
N-TERMINAL MYRISTOYLATION ON GLY-2
no
yes
(MYR)GGKWSKSSVVGWPAVRERMRRAEPAADGVGAASRDLEKHGAITSSNTAANNAACAW(NH2)
XGGKWSKSSVVGWPAVRERMRRAEPAADGVGAASRDLEKHGAITSSNTAANNAACAWX
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
citation
citation_author
pdbx_struct_assembly
pdbx_struct_assembly_prop
pdbx_struct_oper_list
struct_conn
struct_ref_seq_dif
database_2
pdbx_entity_src_syn
pdbx_nmr_software
pdbx_nmr_spectrometer
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Data collection
Database references
Source and taxonomy
Database references
1
0
1999-05-26
1
1
2008-04-26
1
2
2011-07-13
1
3
2019-11-27
1
4
2021-10-27
1
5
2022-12-21
_citation.pdbx_database_id_DOI
_citation.pdbx_database_id_PubMed
_citation.title
_citation_author.name
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_entity_src_syn.details
_pdbx_entity_src_syn.ncbi_taxonomy_id
_pdbx_entity_src_syn.organism_common_name
_pdbx_entity_src_syn.organism_scientific
_pdbx_nmr_software.authors
_pdbx_nmr_software.classification
_pdbx_nmr_spectrometer.manufacturer
_pdbx_nmr_spectrometer.model
_struct_ref_seq_dif.details
RCSB
Y
RCSB
1999-04-12
REL
11676
HIV-1
Human immunodeficiency virus type 1 (isolate NL4-3)
sample
THE COORDINATES OF 2 SIMULATED ANNEALING STRUCTURES ARE PRESENTED IN THIS ENTRY. THE STRUCTURE OF THE
MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN IS HIGHLY FLEXIBLE AND NOT WELL DEFINED BY NMR RESTRAINTS. ONLY TWO
SECONDARY STRUCTURE ELEMENTS CAN BE OBSERVED: A FIRST HELIX IN THE POSITIVE CLUSTER REGION FROM PRO14 TO ARG22
AND A SECOND HELICAL REGION FROM ALA33 TO GLY41. ADDITIONALLY, THE N-TERMINAL MYRISTIC ACID RESIDUE
CLOSELY INTERACTS WITH THE SIDE CHAIN OF TRP5 AND THEREBY FORMS A LOOP WITH GLY2, GLY3 AND LYS4 IN THE
KINK REGION. TWO MODELS ARE PRESENTED TO DEMONSTRATE THE CONFORMATIONAL VARIETY OF THE STRUCTURES CALCULATED.
TWO STRUCTURES WITH LOW TOTAL ENERGY WERE SELECTED SHOWING THE CONFORMATIONAL VARIETY OF THE FLEXIBLE DOMAIN
400
2
1H
4.6
285
K
THE STRUCTURES WERE CALCULATED WITH X-PLOR, V. 3.851 (BRUNGER, 1992) USING A DISTANCE GEOMETRY/SIMULATED ANNEALING PROTOCOL (NILGES ET AL., FEBS LETT. 229, 317 (1988)). THE 3D STRUCTURE OF MYRISTOYLATED HIV-1 NEF ANCHOR
DOMAIN (MYR-2-57) SOLVED BY TWO-DIMENSIONAL HOMONUCLEAR NMR SPECTROSCOPY IS BASED ON 540 EXPERIMENTAL RESTRAINTS:
332 INTRARESIDUAL, 156 SEQUENTIAL AND MEDIUM RANGE (1<=|I-J|<=4), AND 10 LONG RANGE (|I-J|>=5) INTERPROTON
DISTANCE RESTRAINTS; 42 TORSION ANGLE RESTRAINTS (PHI). NO RESTRAINTS FOR HYDROGEN BONDS WERE ADDED.
DISTANCE GEOMETRY, SIMULATED ANNEALING
1
BRUNGER
refinement
X-PLOR
3.851
Neidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzer
structure calculation
AURELIA
2.0
BRUNGER
structure calculation
X-PLOR
3.851
500
Bruker
AMX
800
Bruker
DMX
MYR
1
n
1
MYR
1
A
GLY
2
n
2
GLY
2
A
GLY
3
n
3
GLY
3
A
LYS
4
n
4
LYS
4
A
TRP
5
n
5
TRP
5
A
SER
6
n
6
SER
6
A
LYS
7
n
7
LYS
7
A
SER
8
n
8
SER
8
A
SER
9
n
9
SER
9
A
VAL
10
n
10
VAL
10
A
VAL
11
n
11
VAL
11
A
GLY
12
n
12
GLY
12
A
TRP
13
n
13
TRP
13
A
PRO
14
n
14
PRO
14
A
ALA
15
n
15
ALA
15
A
VAL
16
n
16
VAL
16
A
ARG
17
n
17
ARG
17
A
GLU
18
n
18
GLU
18
A
ARG
19
n
19
ARG
19
A
MET
20
n
20
MET
20
A
ARG
21
n
21
ARG
21
A
ARG
22
n
22
ARG
22
A
ALA
23
n
23
ALA
23
A
GLU
24
n
24
GLU
24
A
PRO
25
n
25
PRO
25
A
ALA
26
n
26
ALA
26
A
ALA
27
n
27
ALA
27
A
ASP
28
n
28
ASP
28
A
GLY
29
n
29
GLY
29
A
VAL
30
n
30
VAL
30
A
GLY
31
n
31
GLY
31
A
ALA
32
n
32
ALA
32
A
ALA
33
n
33
ALA
33
A
SER
34
n
34
SER
34
A
ARG
35
n
35
ARG
35
A
ASP
36
n
36
ASP
36
A
LEU
37
n
37
LEU
37
A
GLU
38
n
38
GLU
38
A
LYS
39
n
39
LYS
39
A
HIS
40
n
40
HIS
40
A
GLY
41
n
41
GLY
41
A
ALA
42
n
42
ALA
42
A
ILE
43
n
43
ILE
43
A
THR
44
n
44
THR
44
A
SER
45
n
45
SER
45
A
SER
46
n
46
SER
46
A
ASN
47
n
47
ASN
47
A
THR
48
n
48
THR
48
A
ALA
49
n
49
ALA
49
A
ALA
50
n
50
ALA
50
A
ASN
51
n
51
ASN
51
A
ASN
52
n
52
ASN
52
A
ALA
53
n
53
ALA
53
A
ALA
54
n
54
ALA
54
A
CYS
55
n
55
CYS
55
A
ALA
56
n
56
ALA
56
A
TRP
57
n
57
TRP
57
A
TRP
57
n
58
NH2
58
A
author_defined_assembly
1
monomeric
310
2
6460
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
identity operation
0.0000000000
0.0000000000
0.0000000000
1
A
ARG
17
0.310
SIDE CHAIN
1
A
ARG
19
0.299
SIDE CHAIN
1
A
ARG
21
0.314
SIDE CHAIN
1
A
ARG
22
0.317
SIDE CHAIN
1
A
ARG
35
0.316
SIDE CHAIN
2
A
ARG
17
0.316
SIDE CHAIN
2
A
ARG
19
0.315
SIDE CHAIN
2
A
ARG
21
0.313
SIDE CHAIN
2
A
ARG
22
0.299
SIDE CHAIN
2
A
ARG
35
0.318
SIDE CHAIN
1
A
SER
6
50.18
86.30
1
A
VAL
11
58.08
154.70
1
A
TRP
13
-159.42
81.03
1
A
PRO
14
-80.66
45.22
1
A
ARG
22
-87.45
-76.13
1
A
ALA
23
155.77
-84.36
1
A
GLU
24
176.77
112.44
1
A
ASP
28
47.03
71.65
1
A
ALA
33
-76.14
-79.78
1
A
SER
34
-87.89
-77.52
1
A
ARG
35
-100.32
-98.68
1
A
ASP
36
-125.66
-62.71
1
A
ALA
49
53.28
-129.50
1
A
ALA
50
53.36
-153.65
1
A
ASN
52
44.17
85.54
1
A
ALA
54
57.99
-167.66
2
A
LYS
4
53.38
104.63
2
A
GLU
18
-53.72
-70.47
2
A
ALA
23
52.57
-170.89
2
A
ALA
27
-125.90
-156.00
2
A
ALA
32
168.35
135.89
2
A
SER
34
-85.44
-89.29
2
A
ARG
35
-108.26
-91.89
2
A
SER
46
-160.78
78.66
2
A
ALA
49
50.32
-145.86
2
A
ALA
50
61.89
128.07
2
A
ASN
51
-131.34
-111.58
2
A
ALA
53
-170.65
-122.50
2
A
ALA
54
63.88
148.20
2
A
CYS
55
-178.53
128.67
2
A
ALA
56
171.61
172.56
MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN, NMR, 2 STRUCTURES
1
N
N
A
VAL
16
A
VAL
16
HELX_P
A
ARG
22
A
ARG
22
1
1
7
A
LEU
37
A
LEU
37
HELX_P
A
GLY
41
A
GLY
41
1
2
5
covale
1.314
both
A
MYR
1
A
C1
MYR
1
1_555
A
GLY
2
A
N
GLY
2
1_555
covale
1.304
both
A
TRP
57
A
C
TRP
57
1_555
A
NH2
58
A
N
NH2
58
1_555
VIRAL PROTEIN
HIV, AIDS, REGULATORY FACTOR, NEGATIVE FACTOR, NEF, MYRISTOYLATION, Viral protein
NEF_HV112
UNP
1
P04324
2
57
1QA5
2
57
P04324
A
1
2
57
1
modified residue
MYR
1
1QA5
A
P04324
1
1
amidation
NH2
58
1QA5
A
P04324
58
1
P 1