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