data_2BRD # _model_server_result.job_id v_v3JmvuYqTU122DEnq6NA _model_server_result.datetime_utc '2024-11-04 18:27:18' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 2brd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":269}' # _entry.id 2BRD # _exptl.entry_id 2BRD _exptl.method 'ELECTRON CRYSTALLOGRAPHY' # _entity.details ? _entity.formula_weight 887.195 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHORIC ACID 2,3-BIS-(3,7,11,15-TETRAMETHYL-HEXADECYLOXY)-PROPYL ESTER 2-HYDROXO-3-PHOSPHONOOXY-PROPYL ESTER' _entity.pdbx_number_of_molecules 10 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 2BRD _cell.length_a 62.45 _cell.length_b 62.45 _cell.length_c 100.9 _cell.Z_PDB 3 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2BRD _symmetry.cell_setting ? _symmetry.Int_Tables_number 143 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 3' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 216 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 216 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id L _struct_conn.ptnr2_label_atom_id C15 _struct_conn.ptnr2_label_comp_id RET _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id RET _struct_conn.ptnr2_auth_seq_id 271 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 1.312 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C46 H96 O11 P2' _chem_comp.formula_weight 887.195 _chem_comp.id DPG _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHORIC ACID 2,3-BIS-(3,7,11,15-TETRAMETHYL-HEXADECYLOXY)-PROPYL ESTER 2-HYDROXO-3-PHOSPHONOOXY-PROPYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DPHPG # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 C2 DPG sing 70 n n C1 O1 DPG sing 71 n n C1 H11 DPG sing 72 n n C1 H12 DPG sing 73 n n C2 C3 DPG sing 74 n n C2 O2 DPG sing 75 n n C2 H2 DPG sing 76 n n C3 O3 DPG sing 77 n n C3 H31 DPG sing 78 n n C3 H32 DPG sing 79 n n C4 C5 DPG sing 80 n n C4 O6 DPG sing 81 n n C4 H41 DPG sing 82 n n C4 H42 DPG sing 83 n n C5 C6 DPG sing 84 n n C5 O7 DPG sing 85 n n C5 H5 DPG sing 86 n n C6 O8 DPG sing 87 n n C6 H61 DPG sing 88 n n C6 H62 DPG sing 89 n n C11 C12 DPG sing 90 n n C11 O1 DPG sing 91 n n C11 H111 DPG sing 92 n n C11 H112 DPG sing 93 n n C12 C13 DPG sing 94 n n C12 H121 DPG sing 95 n n C12 H122 DPG sing 96 n n C13 C14 DPG sing 97 n n C13 C15 DPG sing 98 n n C13 H13 DPG sing 99 n n C14 H141 DPG sing 100 n n C14 H142 DPG sing 101 n n C14 H143 DPG sing 102 n n C15 C16 DPG sing 103 n n C15 H151 DPG sing 104 n n C15 H152 DPG sing 105 n n C16 C17 DPG sing 106 n n C16 H161 DPG sing 107 n n C16 H162 DPG sing 108 n n C17 C18 DPG sing 109 n n C17 H171 DPG sing 110 n n C17 H172 DPG sing 111 n n C18 C19 DPG sing 112 n n C18 C20 DPG sing 113 n n C18 H18 DPG sing 114 n n C19 H191 DPG sing 115 n n C19 H192 DPG sing 116 n n C19 H193 DPG sing 117 n n C20 C21 DPG sing 118 n n C20 H201 DPG sing 119 n n C20 H202 DPG sing 120 n n C21 C22 DPG sing 121 n n C21 H211 DPG sing 122 n n C21 H212 DPG sing 123 n n C22 C23 DPG sing 124 n n C22 H221 DPG sing 125 n n C22 H222 DPG sing 126 n n C23 C24 DPG sing 127 n n C23 C25 DPG sing 128 n n C23 H23 DPG sing 129 n n C24 H241 DPG sing 130 n n C24 H242 DPG sing 131 n n C24 H243 DPG sing 132 n n C25 C26 DPG sing 133 n n C25 H251 DPG sing 134 n n C25 H252 DPG sing 135 n n C26 C27 DPG sing 136 n n C26 H261 DPG sing 137 n n C26 H262 DPG sing 138 n n C27 C28 DPG sing 139 n n C27 H271 DPG sing 140 n n C27 H272 DPG sing 141 n n C28 C29 DPG sing 142 n n C28 C30 DPG sing 143 n n C28 H28 DPG sing 144 n n C29 H291 DPG sing 145 n n C29 H292 DPG sing 146 n n C29 H293 DPG sing 147 n n C30 H301 DPG sing 148 n n C30 H302 DPG sing 149 n n C30 H303 DPG sing 150 n n C41 C42 DPG sing 151 n n C41 O2 DPG sing 152 n n C41 H411 DPG sing 153 n n C41 H412 DPG sing 154 n n C42 C43 DPG sing 155 n n C42 H421 DPG sing 156 n n C42 H422 DPG sing 157 n n C43 C44 DPG sing 158 n n C43 C45 DPG sing 159 n n C43 H43 DPG sing 160 n n C44 H441 DPG sing 161 n n C44 H442 DPG sing 162 n n C44 H443 DPG sing 163 n n C45 C46 DPG sing 164 n n C45 H451 DPG sing 165 n n C45 H452 DPG sing 166 n n C46 C47 DPG sing 167 n n C46 H461 DPG sing 168 n n C46 H462 DPG sing 169 n n C47 C48 DPG sing 170 n n C47 H471 DPG sing 171 n n C47 H472 DPG sing 172 n n C48 C49 DPG sing 173 n n C48 C50 DPG sing 174 n n C48 H48 DPG sing 175 n n C49 H491 DPG sing 176 n n C49 H492 DPG sing 177 n n C49 H493 DPG sing 178 n n C50 C51 DPG sing 179 n n C50 H501 DPG sing 180 n n C50 H502 DPG sing 181 n n C51 C52 DPG sing 182 n n C51 H511 DPG sing 183 n n C51 H512 DPG sing 184 n n C52 C53 DPG sing 185 n n C52 H521 DPG sing 186 n n C52 H522 DPG sing 187 n n C53 C54 DPG sing 188 n n C53 C55 DPG sing 189 n n C53 H53 DPG sing 190 n n C54 H541 DPG sing 191 n n C54 H542 DPG sing 192 n n C54 H543 DPG sing 193 n n C55 C56 DPG sing 194 n n C55 H551 DPG sing 195 n n C55 H552 DPG sing 196 n n C56 C57 DPG sing 197 n n C56 H561 DPG sing 198 n n C56 H562 DPG sing 199 n n C57 C58 DPG sing 200 n n C57 H571 DPG sing 201 n n C57 H572 DPG sing 202 n n C58 C59 DPG sing 203 n n C58 C60 DPG sing 204 n n C58 H58 DPG sing 205 n n C59 H591 DPG sing 206 n n C59 H592 DPG sing 207 n n C59 H593 DPG sing 208 n n C60 H601 DPG sing 209 n n C60 H602 DPG sing 210 n n C60 H603 DPG sing 211 n n O3 P1 DPG sing 212 n n O4 P1 DPG doub 213 n n O5 P1 DPG sing 214 n n O5 HO5 DPG sing 215 n n O6 P1 DPG sing 216 n n O7 HO7 DPG sing 217 n n O8 P2 DPG sing 218 n n O9 P2 DPG doub 219 n n O10 P2 DPG sing 220 n n O10 HO0 DPG sing 221 n n O11 P2 DPG sing 222 n n O11 HO1 DPG sing 223 n n # _atom_sites.entry_id 2BRD _atom_sites.fract_transf_matrix[1][1] 0.016013 _atom_sites.fract_transf_matrix[1][2] 0.009245 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01849 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009911 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 DPG A 1 261 261 DPG DPG . C 2 DPG A 1 262 262 DPG DPG . D 2 DPG A 1 263 263 DPG DPG . E 2 DPG A 1 264 264 DPG DPG . F 2 DPG A 1 265 265 DPG DPG . G 2 DPG A 1 266 266 DPG DPG . H 2 DPG A 1 267 267 DPG DPG . I 2 DPG A 1 268 268 DPG DPG . J 2 DPG A 1 269 269 DPG DPG . K 2 DPG A 1 270 270 DPG DPG . L 3 RET A 1 271 216 RET RET . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 DPG . . . J 2 12.322 -21.195 23.9 1 263.28 ? C1 DPG 269 A 1 HETATM 2 C C2 DPG . . . J 2 11.529 -21.004 25.197 1 286.81 ? C2 DPG 269 A 1 HETATM 3 C C3 DPG . . . J 2 12.354 -20.258 26.241 1 301.69 ? C3 DPG 269 A 1 HETATM 4 C C4 DPG . . . J 2 12.212 -21.833 30.345 1 306.11 ? C4 DPG 269 A 1 HETATM 5 C C5 DPG . . . J 2 13.466 -22.755 30.654 1 301.92 ? C5 DPG 269 A 1 HETATM 6 C C6 DPG . . . J 2 14.718 -22.175 29.936 1 310.54 ? C6 DPG 269 A 1 HETATM 7 C C11 DPG . . . J 2 13.213 -19.241 22.793 1 240.05 ? C11 DPG 269 A 1 HETATM 8 C C12 DPG . . . J 2 12.225 -18.172 23.254 1 250 ? C12 DPG 269 A 1 HETATM 9 C C13 DPG . . . J 2 12.667 -16.752 23.107 1 246.86 ? C13 DPG 269 A 1 HETATM 10 C C14 DPG . . . J 2 13.792 -16.551 24.076 1 266.74 ? C14 DPG 269 A 1 HETATM 11 C C15 DPG . . . J 2 13.094 -16.436 21.693 1 215.29 ? C15 DPG 269 A 1 HETATM 12 C C16 DPG . . . J 2 13.145 -14.957 21.287 1 205.96 ? C16 DPG 269 A 1 HETATM 13 C C17 DPG . . . J 2 14.003 -14.534 20.07 1 178.07 ? C17 DPG 269 A 1 HETATM 14 C C18 DPG . . . J 2 13.743 -13.167 19.354 1 162.19 ? C18 DPG 269 A 1 HETATM 15 C C19 DPG . . . J 2 13.71 -11.977 20.31 1 183.51 ? C19 DPG 269 A 1 HETATM 16 C C20 DPG . . . J 2 12.486 -13.105 18.458 1 143.44 ? C20 DPG 269 A 1 HETATM 17 C C21 DPG . . . J 2 12.761 -12.177 17.278 1 121.59 ? C21 DPG 269 A 1 HETATM 18 C C22 DPG . . . J 2 12.03 -12.584 15.963 1 102.61 ? C22 DPG 269 A 1 HETATM 19 C C23 DPG . . . J 2 12.738 -12.496 14.524 1 90.5 ? C23 DPG 269 A 1 HETATM 20 C C24 DPG . . . J 2 13.806 -13.6 14.459 1 90.2 ? C24 DPG 269 A 1 HETATM 21 C C25 DPG . . . J 2 11.76 -12.79 13.334 1 89.04 ? C25 DPG 269 A 1 HETATM 22 C C26 DPG . . . J 2 12.237 -12.564 11.919 1 99.47 ? C26 DPG 269 A 1 HETATM 23 C C27 DPG . . . J 2 11.699 -13.659 11.061 1 113.17 ? C27 DPG 269 A 1 HETATM 24 C C28 DPG . . . J 2 12.662 -13.969 9.963 1 139.83 ? C28 DPG 269 A 1 HETATM 25 C C29 DPG . . . J 2 12.645 -15.461 9.699 1 147.88 ? C29 DPG 269 A 1 HETATM 26 C C30 DPG . . . J 2 12.409 -13.156 8.688 1 185.02 ? C30 DPG 269 A 1 HETATM 27 C C41 DPG . . . J 2 12.192 -22.91 26.521 1 304.93 ? C41 DPG 269 A 1 HETATM 28 C C42 DPG . . . J 2 12.549 -24.204 25.741 1 295.09 ? C42 DPG 269 A 1 HETATM 29 C C43 DPG . . . J 2 14.03 -24.656 25.516 1 291.8 ? C43 DPG 269 A 1 HETATM 30 C C44 DPG . . . J 2 14.436 -25.463 26.794 1 307.75 ? C44 DPG 269 A 1 HETATM 31 C C45 DPG . . . J 2 14.213 -25.376 24.113 1 267.46 ? C45 DPG 269 A 1 HETATM 32 C C46 DPG . . . J 2 15.604 -25.361 23.361 1 252.25 ? C46 DPG 269 A 1 HETATM 33 C C47 DPG . . . J 2 15.574 -25.585 21.818 1 218.16 ? C47 DPG 269 A 1 HETATM 34 C C48 DPG . . . J 2 16.696 -24.976 20.946 1 198.1 ? C48 DPG 269 A 1 HETATM 35 C C49 DPG . . . J 2 16.68 -23.435 21.017 1 199.73 ? C49 DPG 269 A 1 HETATM 36 C C50 DPG . . . J 2 16.482 -25.48 19.516 1 165.73 ? C50 DPG 269 A 1 HETATM 37 C C51 DPG . . . J 2 17.585 -25.072 18.538 1 145.05 ? C51 DPG 269 A 1 HETATM 38 C C52 DPG . . . J 2 17.119 -24.884 17.092 1 118.52 ? C52 DPG 269 A 1 HETATM 39 C C53 DPG . . . J 2 17.818 -23.715 16.272 1 106.46 ? C53 DPG 269 A 1 HETATM 40 C C54 DPG . . . J 2 19.351 -23.856 15.906 1 101.94 ? C54 DPG 269 A 1 HETATM 41 C C55 DPG . . . J 2 16.963 -23.355 14.999 1 93.35 ? C55 DPG 269 A 1 HETATM 42 C C56 DPG . . . J 2 17.053 -21.888 14.519 1 90.47 ? C56 DPG 269 A 1 HETATM 43 C C57 DPG . . . J 2 16.965 -21.654 13.011 1 90.18 ? C57 DPG 269 A 1 HETATM 44 C C58 DPG . . . J 2 17.464 -20.214 12.784 1 91.41 ? C58 DPG 269 A 1 HETATM 45 C C59 DPG . . . J 2 18.99 -20.109 12.6 1 92.66 ? C59 DPG 269 A 1 HETATM 46 C C60 DPG . . . J 2 16.683 -19.405 11.727 1 102.02 ? C60 DPG 269 A 1 HETATM 47 O O1 DPG . . . J 2 13.39 -20.214 23.858 1 262.44 ? O1 DPG 269 A 1 HETATM 48 O O2 DPG . . . J 2 11.159 -22.27 25.738 1 295.05 ? O2 DPG 269 A 1 HETATM 49 O O3 DPG . . . J 2 11.444 -19.649 27.18 1 311.14 ? O3 DPG 269 A 1 HETATM 50 O O4 DPG . . . J 2 10.668 -19.086 29.44 1 314.26 ? O4 DPG 269 A 1 HETATM 51 O O5 DPG . . . J 2 13.121 -18.698 29.012 1 316.1 ? O5 DPG 269 A 1 HETATM 52 O O6 DPG . . . J 2 12.158 -21.153 29.039 1 316.02 ? O6 DPG 269 A 1 HETATM 53 O O7 DPG . . . J 2 13.329 -24.157 30.264 1 307.09 ? O7 DPG 269 A 1 HETATM 54 O O8 DPG . . . J 2 15.799 -21.969 30.877 1 298.42 ? O8 DPG 269 A 1 HETATM 55 O O9 DPG . . . J 2 18.153 -22.701 30.127 1 308.63 ? O9 DPG 269 A 1 HETATM 56 O O10 DPG . . . J 2 17.125 -20.616 29.145 1 315.66 ? O10 DPG 269 A 1 HETATM 57 O O11 DPG . . . J 2 17.847 -20.617 31.49 1 286.68 ? O11 DPG 269 A 1 HETATM 58 P P1 DPG . . . J 2 11.891 -19.536 28.746 1 316.63 ? P1 DPG 269 A 1 HETATM 59 P P2 DPG . . . J 2 17.282 -21.475 30.385 1 305.61 ? P2 DPG 269 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 59 #