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