1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Tugarinov, V. Zvi, A. Levy, R. Anglister, J. 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 C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C2 H5 N O2 75.067 y GLYCINE 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 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 C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N C N 48 N O N 49 N N N 50 N O N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N N N 62 N C N 63 N C N 64 N O N 65 N O N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N N N 72 S C N 73 N C N 74 N O N 75 S C N 76 N C N 77 N C N 78 N C N 79 N O N 80 N H N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N N N 94 S C N 95 N C N 96 N O N 97 N C N 98 N C N 99 N C N 100 N C N 101 N N N 102 N O N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N N N 119 S C N 120 N C N 121 N O N 122 N C Y 123 N C Y 124 N C Y 125 N C Y 126 N C Y 127 N C Y 128 N C N 129 N O N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N N N 142 S C N 143 N C N 144 N O N 145 N C N 146 N C N 147 N C N 148 N O N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N N N 159 S C N 160 N C N 161 N O N 162 N C N 163 N O N 164 N O N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N N N 173 S C N 174 N C N 175 N O N 176 R C N 177 N O N 178 N C N 179 N O N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N N N 190 S C N 191 N C N 192 N O N 193 N C N 194 N C N 195 N C N 196 N O N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H N 206 N H N 207 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N doub N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N doub N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N doub N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N doub N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N doub N 119 N sing N 120 N sing N 121 N sing N 122 N sing Y 123 N doub Y 124 N sing Y 125 N sing N 126 N sing Y 127 N doub N 128 N sing Y 129 N doub N 130 N sing Y 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N doub N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N doub N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N doub N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N doub N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing US Nat.Struct.Biol. NSBIEW 2024 1072-8368 6 331 335 10.1038/7567 10201400 A cis proline turn linking two beta-hairpin strands in the solution structure of an antibody-bound HIV-1IIIB V3 peptide. 1999 US Biochemistry BICHAW 0033 0006-2960 36 8619 8627 Conformation of the Principal Neutralizing Determinant of Human Immunodeficiency Virus Type 1 in Complex with an Anti-GP120 Virus Neutralizing Antibody Studied by Two-dimensional Nuclear Magnetic Resonance Difference Spectroscopy. 1997 10.2210/pdb1b03/pdb pdb_00001b03 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 P1053 PEPTIDE REPRESENTS THE FULL ANTIBODY RECOGNIZED EPITOPE OF THE HIV-1IIIB GP120 V3 LOOP. 2017.406 PROTEIN (P1053 PEPTIDE) 1 syn polymer no no RKSIRIQRGPGRAFVTIG RKSIRIQRGPGRAFVTIG A polypeptide(L) n n n n n n n n n n n n n n n n n n pdbx_struct_assembly pdbx_struct_oper_list struct_conf chem_comp_atom chem_comp_bond database_2 pdbx_nmr_software repository Initial release Version format compliance Version format compliance Derived calculations Data collection Database references 1 0 1998-11-25 1 1 2008-04-26 1 2 2011-07-13 1 3 2017-11-29 1 4 2023-12-27 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name Y RCSB 1998-11-17 REL REL THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. sample THE STRUCTURE WAS DETERMINED IN COMPLEX WITH THE FV ANTIBODY FRAGMENT USING ISOTOPE-FILTERED AND ISOTOPE-EDITED NMR WITH EITHER THE FV OR THE PEPTIDE LABELLED WITH 15N AND 13C. LEAST RESTRAINT VIOLATIONS 35 15N 13C FILTERED NOESY 7.1 305 K AFTER INITIAL SIMULATED ANNEALING CALCULATIONS THE STRUCTURES WERE MINIMIZED USING A FULL L-J POTENTIAL REPRESENTATION. THE CIS PEPTIDE BOND BETWEEN GLY 12 AND PRO 13 WAS PATHED CIS IN THE PROCESS OF STRUCTURE GENERATION. HYBRID DG-SA BRUNGER refinement X-PLOR 3.1 structure solution NMRPipe 600 Bruker DMX600 ARG 4 n 1 ARG 4 A LYS 5 n 2 LYS 5 A SER 6 n 3 SER 6 A ILE 7 n 4 ILE 7 A ARG 8 n 5 ARG 8 A ILE 9 n 6 ILE 9 A GLN 10 n 7 GLN 10 A ARG 11 n 8 ARG 11 A GLY 12 n 9 GLY 12 A PRO 13 n 10 PRO 13 A GLY 14 n 11 GLY 14 A ARG 15 n 12 ARG 15 A ALA 16 n 13 ALA 16 A PHE 17 n 14 PHE 17 A VAL 18 n 15 VAL 18 A THR 19 n 16 THR 19 A ILE 20 n 17 ILE 20 A GLY 21 n 18 GLY 21 A author_defined_assembly 1 monomeric 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 A O LYS 5 A O LYS 2 A N ILE 20 A N ILE 17 2 A ALA 16 -169.52 -166.47 4 A ARG 15 -62.28 88.22 5 A ALA 16 -170.28 -168.12 6 A ALA 16 -160.48 -165.16 8 A ALA 16 -160.96 -169.32 10 A ALA 16 -168.85 -166.63 14 A ALA 16 -170.42 -168.13 19 A ALA 16 -163.29 -168.86 21 A ALA 16 -170.22 -174.74 23 A ALA 16 -168.31 -164.61 35 A ARG 15 -61.58 98.84 SOLUTION STRUCTURE OF THE ANTIBODY-BOUND HIV-1IIIB V3 PEPTIDE 1 N N VIRAL PROTEIN P1053 STRUCTURE, Viral protein A GLY 12 A GLY 9 1 A PRO 13 A PRO 10 0.07 A GLY 12 A GLY 9 2 A PRO 13 A PRO 10 0.14 A GLY 12 A GLY 9 3 A PRO 13 A PRO 10 0.04 A GLY 12 A GLY 9 4 A PRO 13 A PRO 10 0.01 A GLY 12 A GLY 9 5 A PRO 13 A PRO 10 0.18 A GLY 12 A GLY 9 6 A PRO 13 A PRO 10 0.13 A GLY 12 A GLY 9 7 A PRO 13 A PRO 10 0.12 A GLY 12 A GLY 9 8 A PRO 13 A PRO 10 0.13 A GLY 12 A GLY 9 9 A PRO 13 A PRO 10 -0.15 A GLY 12 A GLY 9 10 A PRO 13 A PRO 10 -0.07 A GLY 12 A GLY 9 11 A PRO 13 A PRO 10 0.06 A GLY 12 A GLY 9 12 A PRO 13 A PRO 10 -0.05 A GLY 12 A GLY 9 13 A PRO 13 A PRO 10 -0.03 A GLY 12 A GLY 9 14 A PRO 13 A PRO 10 0.11 A GLY 12 A GLY 9 15 A PRO 13 A PRO 10 0.00 A GLY 12 A GLY 9 16 A PRO 13 A PRO 10 -0.11 A GLY 12 A GLY 9 17 A PRO 13 A PRO 10 -0.02 A GLY 12 A GLY 9 18 A PRO 13 A PRO 10 0.24 A GLY 12 A GLY 9 19 A PRO 13 A PRO 10 0.16 A GLY 12 A GLY 9 20 A PRO 13 A PRO 10 -0.02 A GLY 12 A GLY 9 21 A PRO 13 A PRO 10 0.13 A GLY 12 A GLY 9 22 A PRO 13 A PRO 10 0.17 A GLY 12 A GLY 9 23 A PRO 13 A PRO 10 0.00 A GLY 12 A GLY 9 24 A PRO 13 A PRO 10 0.02 A GLY 12 A GLY 9 25 A PRO 13 A PRO 10 0.03 A GLY 12 A GLY 9 26 A PRO 13 A PRO 10 0.08 A GLY 12 A GLY 9 27 A PRO 13 A PRO 10 0.35 A GLY 12 A GLY 9 28 A PRO 13 A PRO 10 0.24 A GLY 12 A GLY 9 29 A PRO 13 A PRO 10 -0.17 A GLY 12 A GLY 9 30 A PRO 13 A PRO 10 0.04 A GLY 12 A GLY 9 31 A PRO 13 A PRO 10 -0.07 A GLY 12 A GLY 9 32 A PRO 13 A PRO 10 -0.12 A GLY 12 A GLY 9 33 A PRO 13 A PRO 10 0.05 A GLY 12 A GLY 9 34 A PRO 13 A PRO 10 -0.02 A GLY 12 A GLY 9 35 A PRO 13 A PRO 10 0.31 Q79428_9HIV1 UNP 1 Q79428 108 125 1B03 4 21 Q79428 A 1 1 18 2 anti-parallel A LYS 5 A LYS 2 A ILE 9 A ILE 6 A ALA 16 A ALA 13 A ILE 20 A ILE 17 1 P 1