data_6DNF # _model_server_result.job_id EZtCci0dKel6aATlyv0pJw _model_server_result.datetime_utc '2024-11-04 23:28:05' _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 6dnf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 6DNF # _exptl.entry_id 6DNF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 734.981 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_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,M,N,O _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 H N N ? 2 J N N ? 2 K N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 O N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order metalc ? metalc1 A OE1 GLU 228 A GLU 228 1_555 G CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.718 ? metalc ? metalc2 A OE2 GLU 228 A GLU 228 1_555 G CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc3 G CA CA . A CA 403 1_555 B OE1 GLU 228 B GLU 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.955 ? metalc ? metalc4 G CA CA . A CA 403 1_555 B OE2 GLU 228 B GLU 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc5 G CA CA . A CA 403 1_555 C OE1 GLU 228 C GLU 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? metalc ? metalc6 G CA CA . A CA 403 1_555 C OE2 GLU 228 C GLU 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc7 G CA CA . A CA 403 1_555 D OE1 GLU 228 D GLU 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.984 ? metalc ? metalc8 G CA CA . A CA 403 1_555 D OE2 GLU 228 D GLU 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? # _chem_comp.formula 'C39 H75 O10 P' _chem_comp.formula_weight 734.981 _chem_comp.id DGG _chem_comp.mon_nstd_flag . _chem_comp.name 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C16 C15 DGG sing 83 n n C16 H161 DGG sing 84 n n C16 H162 DGG sing 85 n n C16 H163 DGG sing 86 n n C15 C14 DGG sing 87 n n C15 H151 DGG sing 88 n n C15 H152 DGG sing 89 n n C14 C13 DGG sing 90 n n C14 H141 DGG sing 91 n n C14 H142 DGG sing 92 n n C13 C12 DGG sing 93 n n C13 H131 DGG sing 94 n n C13 H132 DGG sing 95 n n C12 C11 DGG sing 96 n n C12 H121 DGG sing 97 n n C12 H122 DGG sing 98 n n C11 C10 DGG sing 99 n n C11 H111 DGG sing 100 n n C11 H112 DGG sing 101 n n C10 C9 DGG sing 102 n n C10 H101 DGG sing 103 n n C10 H102 DGG sing 104 n n C9 C8 DGG sing 105 n n C9 HC91 DGG sing 106 n n C9 HC92 DGG sing 107 n n C8 C7 DGG sing 108 n n C8 HC81 DGG sing 109 n n C8 HC82 DGG sing 110 n n C7 C6 DGG sing 111 n n C7 HC71 DGG sing 112 n n C7 HC72 DGG sing 113 n n C6 C5 DGG sing 114 n n C6 HC61 DGG sing 115 n n C6 HC62 DGG sing 116 n n C5 C4 DGG sing 117 n n C5 HC51 DGG sing 118 n n C5 HC52 DGG sing 119 n n C4 C3 DGG sing 120 n n C4 HC41 DGG sing 121 n n C4 HC42 DGG sing 122 n n C3 C2 DGG sing 123 n n C3 HC31 DGG sing 124 n n C3 HC32 DGG sing 125 n n C2 C1 DGG sing 126 n n C2 HC21 DGG sing 127 n n C2 HC22 DGG sing 128 n n C1 O1 DGG doub 129 n n C1 O17 DGG sing 130 n n O17 C17 DGG sing 131 n n C17 C19 DGG sing 132 n n C17 H171 DGG sing 133 n n C17 H172 DGG sing 134 n n C19 O19 DGG sing 135 n n C19 C18 DGG sing 136 n n C19 H191 DGG sing 137 n n O19 C21 DGG sing 138 n n C21 O21 DGG doub 139 n n C21 C22 DGG sing 140 n n C22 C23 DGG sing 141 n n C22 H221 DGG sing 142 n n C22 H222 DGG sing 143 n n C23 C24 DGG sing 144 n n C23 H231 DGG sing 145 n n C23 H232 DGG sing 146 n n C24 C25 DGG sing 147 n n C24 H241 DGG sing 148 n n C24 H242 DGG sing 149 n n C25 C26 DGG sing 150 n n C25 H251 DGG sing 151 n n C25 H252 DGG sing 152 n n C26 C27 DGG sing 153 n n C26 H261 DGG sing 154 n n C26 H262 DGG sing 155 n n C27 C28 DGG sing 156 n n C27 H271 DGG sing 157 n n C27 H272 DGG sing 158 n n C28 C29 DGG sing 159 n n C28 H281 DGG sing 160 n n C28 H282 DGG sing 161 n n C29 C30 DGG sing 162 n n C29 C39 DGG sing 163 n n C29 H291 DGG sing 164 n n C30 C39 DGG sing 165 n n C30 C31 DGG sing 166 n n C30 H301 DGG sing 167 n n C39 H391 DGG sing 168 n n C39 H392 DGG sing 169 n n C31 C32 DGG sing 170 n n C31 H311 DGG sing 171 n n C31 H312 DGG sing 172 n n C32 C33 DGG sing 173 n n C32 H321 DGG sing 174 n n C32 H322 DGG sing 175 n n C33 C34 DGG sing 176 n n C33 H331 DGG sing 177 n n C33 H332 DGG sing 178 n n C34 C35 DGG sing 179 n n C34 H341 DGG sing 180 n n C34 H342 DGG sing 181 n n C35 C36 DGG sing 182 n n C35 H351 DGG sing 183 n n C35 H352 DGG sing 184 n n C36 H361 DGG sing 185 n n C36 H362 DGG sing 186 n n C36 H363 DGG sing 187 n n C18 OP2 DGG sing 188 n n C18 H181 DGG sing 189 n n C18 H182 DGG sing 190 n n P OP1 DGG sing 191 n n P OP2 DGG sing 192 n n P OP3 DGG doub 193 n n P OP4 DGG sing 194 n n OP1 HOP1 DGG sing 195 n n OP4 C40 DGG sing 196 n n C40 C41 DGG sing 197 n n C40 H401 DGG sing 198 n n C40 H402 DGG sing 199 n n C41 O42 DGG sing 200 n n C41 C43 DGG sing 201 n n C41 H411 DGG sing 202 n n O42 H421 DGG sing 203 n n C43 O44 DGG sing 204 n n C43 H431 DGG sing 205 n n C43 H432 DGG sing 206 n n O44 H441 DGG sing 207 n n # _atom_sites.entry_id 6DNF _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _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] 1 _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 E 2 DGG A 1 401 500 DGG PGW . F 3 CA A 1 402 511 CA CA . G 3 CA A 1 403 512 CA CA . H 2 DGG A 1 404 501 DGG PGW . I 3 CA B 1 401 513 CA CA . J 2 DGG B 1 402 501 DGG PGW . K 2 DGG B 1 403 500 DGG PGW . L 2 DGG C 1 501 501 DGG PGW . M 2 DGG C 1 502 500 DGG PGW . N 2 DGG D 1 501 501 DGG PGW . O 2 DGG D 1 502 500 DGG PGW . # 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 C10 DGG . . . E 2 157.832 149.656 207.653 1 155.48 ? C10 DGG 401 A 1 HETATM 2 C C9 DGG . . . E 2 158.698 149.699 208.906 1 155.48 ? C9 DGG 401 A 1 HETATM 3 C C8 DGG . . . E 2 157.842 149.654 210.166 1 155.48 ? C8 DGG 401 A 1 HETATM 4 C C7 DGG . . . E 2 158.706 149.743 211.417 1 155.48 ? C7 DGG 401 A 1 HETATM 5 C C6 DGG . . . E 2 157.851 149.68 212.677 1 155.48 ? C6 DGG 401 A 1 HETATM 6 C C5 DGG . . . E 2 158.714 149.781 213.929 1 155.48 ? C5 DGG 401 A 1 HETATM 7 C C4 DGG . . . E 2 157.868 149.62 215.186 1 155.48 ? C4 DGG 401 A 1 HETATM 8 C C3 DGG . . . E 2 158.728 149.7 216.442 1 155.48 ? C3 DGG 401 A 1 HETATM 9 C C2 DGG . . . E 2 157.893 149.422 217.686 1 155.48 ? C2 DGG 401 A 1 HETATM 10 C C1 DGG . . . E 2 158.748 149.555 218.923 1 155.48 ? C1 DGG 401 A 1 HETATM 11 O O1 DGG . . . E 2 158.448 150.345 219.803 1 155.48 ? O1 DGG 401 A 1 HETATM 12 O O17 DGG . . . E 2 159.939 148.737 219.086 1 155.48 ? O17 DGG 401 A 1 HETATM 13 C C17 DGG . . . E 2 160.57 148.652 220.362 1 155.48 ? C17 DGG 401 A 1 HETATM 14 C C19 DGG . . . E 2 161.861 147.849 220.253 1 155.48 ? C19 DGG 401 A 1 HETATM 15 O O19 DGG . . . E 2 162.815 148.576 219.48 1 155.48 ? O19 DGG 401 A 1 HETATM 16 C C21 DGG . . . E 2 163.904 147.73 219.017 1 155.48 ? C21 DGG 401 A 1 HETATM 17 O O21 DGG . . . E 2 164.137 146.684 219.6 1 155.48 ? O21 DGG 401 A 1 HETATM 18 C C22 DGG . . . E 2 164.738 148.148 217.83 1 155.48 ? C22 DGG 401 A 1 HETATM 19 C C23 DGG . . . E 2 163.87 148.165 216.578 1 155.48 ? C23 DGG 401 A 1 HETATM 20 C C24 DGG . . . E 2 164.711 148.393 215.328 1 155.48 ? C24 DGG 401 A 1 HETATM 21 C C25 DGG . . . E 2 163.856 148.278 214.072 1 155.48 ? C25 DGG 401 A 1 HETATM 22 C C26 DGG . . . E 2 164.713 148.363 212.814 1 155.48 ? C26 DGG 401 A 1 HETATM 23 C C27 DGG . . . E 2 163.866 148.158 211.564 1 155.48 ? C27 DGG 401 A 1 HETATM 24 C C28 DGG . . . E 2 164.725 148.206 210.307 1 155.48 ? C28 DGG 401 A 1 HETATM 25 C C18 DGG . . . E 2 162.417 147.58 221.646 1 155.48 ? C18 DGG 401 A 1 HETATM 26 P P DGG . . . E 2 162.819 148.742 223.971 1 155.48 ? P DGG 401 A 1 HETATM 27 O OP1 DGG . . . E 2 164.256 148.304 224.12 1 155.48 ? OP1 DGG 401 A 1 HETATM 28 O OP2 DGG . . . E 2 162.469 148.789 222.4 1 155.48 ? OP2 DGG 401 A 1 HETATM 29 O OP3 DGG . . . E 2 161.724 147.977 224.675 1 155.48 ? OP3 DGG 401 A 1 HETATM 30 O OP4 DGG . . . E 2 162.719 150.286 224.415 1 155.48 ? OP4 DGG 401 A 1 HETATM 31 C C40 DGG . . . E 2 162.758 150.64 225.796 1 155.48 ? C40 DGG 401 A 1 HETATM 32 C C41 DGG . . . E 2 162.788 152.157 225.94 1 155.48 ? C41 DGG 401 A 1 HETATM 33 O O42 DGG . . . E 2 164.105 152.572 226.321 1 155.48 ? O42 DGG 401 A 1 HETATM 34 H HC91 DGG . . . E 2 159.385 148.85 208.903 1 155.48 ? HC91 DGG 401 A 1 HETATM 35 H HC92 DGG . . . E 2 159.295 150.613 208.905 1 155.48 ? HC92 DGG 401 A 1 HETATM 36 H HC81 DGG . . . E 2 157.132 150.483 210.153 1 155.48 ? HC81 DGG 401 A 1 HETATM 37 H HC82 DGG . . . E 2 157.27 148.723 210.184 1 155.48 ? HC82 DGG 401 A 1 HETATM 38 H HC71 DGG . . . E 2 159.424 148.921 211.423 1 155.48 ? HC71 DGG 401 A 1 HETATM 39 H HC72 DGG . . . E 2 159.268 150.679 211.405 1 155.48 ? HC72 DGG 401 A 1 HETATM 40 H HC61 DGG . . . E 2 157.128 150.498 212.667 1 155.48 ? HC61 DGG 401 A 1 HETATM 41 H HC62 DGG . . . E 2 157.295 148.741 212.693 1 155.48 ? HC62 DGG 401 A 1 HETATM 42 H HC51 DGG . . . E 2 159.482 149.005 213.906 1 155.48 ? HC51 DGG 401 A 1 HETATM 43 H HC52 DGG . . . E 2 159.216 150.75 213.949 1 155.48 ? HC52 DGG 401 A 1 HETATM 44 H HC41 DGG . . . E 2 157.109 150.405 215.216 1 155.48 ? HC41 DGG 401 A 1 HETATM 45 H HC42 DGG . . . E 2 157.354 148.657 215.158 1 155.48 ? HC42 DGG 401 A 1 HETATM 46 H HC31 DGG . . . E 2 159.538 148.971 216.376 1 155.48 ? HC31 DGG 401 A 1 HETATM 47 H HC32 DGG . . . E 2 159.174 150.693 216.516 1 155.48 ? HC32 DGG 401 A 1 HETATM 48 H HC21 DGG . . . E 2 157.062 150.128 217.736 1 155.48 ? HC21 DGG 401 A 1 HETATM 49 H HC22 DGG . . . E 2 157.479 148.413 217.633 1 155.48 ? HC22 DGG 401 A 1 HETATM 50 H H171 DGG . . . E 2 159.896 148.171 221.074 1 155.48 ? H171 DGG 401 A 1 HETATM 51 H H172 DGG . . . E 2 160.791 149.656 220.73 1 155.48 ? H172 DGG 401 A 1 HETATM 52 H H191 DGG . . . E 2 161.64 146.888 219.767 1 155.48 ? H191 DGG 401 A 1 HETATM 53 H H221 DGG . . . E 2 165.566 147.449 217.695 1 155.48 ? H221 DGG 401 A 1 HETATM 54 H H222 DGG . . . E 2 165.156 149.142 218.003 1 155.48 ? H222 DGG 401 A 1 HETATM 55 H H231 DGG . . . E 2 163.124 148.959 216.664 1 155.48 ? H231 DGG 401 A 1 HETATM 56 H H232 DGG . . . E 2 163.339 147.215 216.491 1 155.48 ? H232 DGG 401 A 1 HETATM 57 H H241 DGG . . . E 2 165.516 147.656 215.291 1 155.48 ? H241 DGG 401 A 1 HETATM 58 H H242 DGG . . . E 2 165.165 149.385 215.37 1 155.48 ? H242 DGG 401 A 1 HETATM 59 H H251 DGG . . . E 2 163.114 149.079 214.061 1 155.48 ? H251 DGG 401 A 1 HETATM 60 H H252 DGG . . . E 2 163.321 147.326 214.082 1 155.48 ? H252 DGG 401 A 1 HETATM 61 H H261 DGG . . . E 2 165.495 147.602 212.854 1 155.48 ? H261 DGG 401 A 1 HETATM 62 H H262 DGG . . . E 2 165.197 149.341 212.769 1 155.48 ? H262 DGG 401 A 1 HETATM 63 H H271 DGG . . . E 2 163.1 148.934 211.512 1 155.48 ? H271 DGG 401 A 1 HETATM 64 H H272 DGG . . . E 2 163.36 147.191 211.622 1 155.48 ? H272 DGG 401 A 1 HETATM 65 H H181 DGG . . . E 2 163.419 147.154 221.565 1 155.48 ? H181 DGG 401 A 1 HETATM 66 H H182 DGG . . . E 2 161.782 146.855 222.16 1 155.48 ? H182 DGG 401 A 1 HETATM 67 H H401 DGG . . . E 2 161.879 150.239 226.303 1 155.48 ? H401 DGG 401 A 1 HETATM 68 H H402 DGG . . . E 2 163.646 150.208 226.262 1 155.48 ? H402 DGG 401 A 1 HETATM 69 H H421 DGG . . . E 2 164.737 152.3 225.642 1 155.48 ? H421 DGG 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 69 #