data_6K7M # _model_server_result.job_id FISgTLuSW1AhYu7UdRDxhw _model_server_result.datetime_utc '2024-11-22 05:31:00' _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 6k7m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1304}' # _entry.id 6K7M # _exptl.entry_id 6K7M _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 762.006 _entity.id 7 _entity.src_method man _entity.type non-polymer _entity.pdbx_description '(2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid' _entity.pdbx_number_of_molecules 1 _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 90 _cell.entry_id 6K7M _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6K7M _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 MAN NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 B 1 NAG C 401 NAG 3 n C NAG 2 B 2 NAG C 402 NAG 3 n C MAN 3 B 3 MAN C 403 MAN # 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 disulf ? disulf1 B SG CYS 91 C CYS 91 1_555 B SG CYS 104 C CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 B SG CYS 94 C CYS 94 1_555 B SG CYS 102 C CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 B SG CYS 157 C CYS 157 1_555 B SG CYS 171 C CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 B ND2 ASN 107 C ASN 107 1_555 I C1 NAG . C NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 B ND2 ASN 180 C ASN 180 1_555 C C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale3 B ND2 ASN 294 C ASN 294 1_555 H C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale4 C O4 NAG . B NAG 1 1_555 C C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 C O4 NAG . B NAG 2 1_555 C C1 MAN . B MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? metalc ? metalc1 A OD2 ASP 414 A ASP 409 1_555 F MG MG . A MG 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.892 ? metalc ? metalc2 A O THR 416 A THR 411 1_555 F MG MG . A MG 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc3 A OD1 ASP 791 A ASP 786 1_555 F MG MG . A MG 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? # _chem_comp.formula 'C40 H76 N O10 P' _chem_comp.formula_weight 762.006 _chem_comp.id D39 _chem_comp.mon_nstd_flag . _chem_comp.name '(2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid' _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 N C D39 sing 87 n n O9 C39 D39 doub 88 n n C C39 D39 sing 89 n n C C1 D39 sing 90 n n C39 O8 D39 sing 91 n n C1 O D39 sing 92 n n O P D39 sing 93 n n O1 P D39 doub 94 n n O5 C5 D39 doub 95 n n C2 O3 D39 sing 96 n n C2 C3 D39 sing 97 n n P O3 D39 sing 98 n n P O2 D39 sing 99 n n C4 C3 D39 sing 100 n n C4 O4 D39 sing 101 n n C5 O4 D39 sing 102 n n C5 C6 D39 sing 103 n n C3 O6 D39 sing 104 n n O6 C21 D39 sing 105 n n C6 C7 D39 sing 106 n n C21 C22 D39 sing 107 n n C21 O7 D39 doub 108 n n C22 C23 D39 sing 109 n n C7 C8 D39 sing 110 n n C8 C9 D39 sing 111 n n C23 C24 D39 sing 112 n n C24 C25 D39 sing 113 n n C9 C10 D39 sing 114 n n C25 C26 D39 sing 115 n n C10 C11 D39 sing 116 n n C28 C29 D39 sing 117 n n C28 C27 D39 sing 118 n n C26 C27 D39 sing 119 n n C11 C12 D39 sing 120 n n C29 C30 D39 doub 121 z n C12 C13 D39 sing 122 n n C13 C14 D39 sing 123 n n C35 C34 D39 sing 124 n n C35 C36 D39 sing 125 n n C30 C31 D39 sing 126 n n C34 C33 D39 sing 127 n n C31 C32 D39 sing 128 n n C15 C14 D39 sing 129 n n C15 C16 D39 sing 130 n n C36 C37 D39 sing 131 n n C33 C32 D39 sing 132 n n C37 C38 D39 sing 133 n n C16 C17 D39 sing 134 n n C17 C18 D39 sing 135 n n C19 C18 D39 sing 136 n n C19 C20 D39 sing 137 n n C4 H1 D39 sing 138 n n C4 H2 D39 sing 139 n n C6 H3 D39 sing 140 n n C6 H4 D39 sing 141 n n C7 H5 D39 sing 142 n n C7 H6 D39 sing 143 n n C8 H7 D39 sing 144 n n C8 H8 D39 sing 145 n n C9 H9 D39 sing 146 n n C9 H10 D39 sing 147 n n C10 H11 D39 sing 148 n n C10 H12 D39 sing 149 n n C11 H13 D39 sing 150 n n C11 H14 D39 sing 151 n n C12 H15 D39 sing 152 n n C12 H16 D39 sing 153 n n C13 H17 D39 sing 154 n n C13 H18 D39 sing 155 n n C14 H19 D39 sing 156 n n C14 H20 D39 sing 157 n n O8 H21 D39 sing 158 n n C15 H22 D39 sing 159 n n C15 H23 D39 sing 160 n n N H24 D39 sing 161 n n N H25 D39 sing 162 n n C H27 D39 sing 163 n n C1 H28 D39 sing 164 n n C1 H29 D39 sing 165 n n C16 H30 D39 sing 166 n n C16 H31 D39 sing 167 n n C17 H32 D39 sing 168 n n C17 H33 D39 sing 169 n n C18 H34 D39 sing 170 n n C18 H35 D39 sing 171 n n C19 H36 D39 sing 172 n n C19 H37 D39 sing 173 n n C2 H38 D39 sing 174 n n C2 H39 D39 sing 175 n n C20 H40 D39 sing 176 n n C20 H41 D39 sing 177 n n C20 H42 D39 sing 178 n n C22 H43 D39 sing 179 n n C22 H44 D39 sing 180 n n C23 H45 D39 sing 181 n n C23 H46 D39 sing 182 n n C24 H47 D39 sing 183 n n C24 H48 D39 sing 184 n n C25 H49 D39 sing 185 n n C25 H50 D39 sing 186 n n C26 H51 D39 sing 187 n n C26 H52 D39 sing 188 n n C27 H53 D39 sing 189 n n C27 H54 D39 sing 190 n n C28 H55 D39 sing 191 n n C28 H56 D39 sing 192 n n C29 H57 D39 sing 193 n n C3 H58 D39 sing 194 n n C30 H59 D39 sing 195 n n C31 H60 D39 sing 196 n n C31 H61 D39 sing 197 n n C32 H62 D39 sing 198 n n C32 H63 D39 sing 199 n n C33 H64 D39 sing 200 n n C33 H65 D39 sing 201 n n C34 H66 D39 sing 202 n n C34 H67 D39 sing 203 n n C35 H68 D39 sing 204 n n C35 H69 D39 sing 205 n n C36 H70 D39 sing 206 n n C36 H71 D39 sing 207 n n C37 H72 D39 sing 208 n n C37 H73 D39 sing 209 n n C38 H74 D39 sing 210 n n C38 H75 D39 sing 211 n n C38 H76 D39 sing 212 n n O2 H77 D39 sing 213 n n # _atom_sites.entry_id 6K7M _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 D 4 ALF A 1 1301 1301 ALF ALF . E 5 Y01 A 1 1302 501 Y01 Y01 . F 6 MG A 1 1303 1 MG MG . G 7 D39 A 1 1304 1 D39 XXX . H 8 NAG C 1 401 404 NAG NAG . I 8 NAG C 1 402 405 NAG NAG . # 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 O O3 D39 . . . G 7 107.9 120 103.086 1 41.41 ? O3 D39 1304 A 1 HETATM 2 C C4 D39 . . . G 7 105.884 123.065 102.685 1 41.41 ? C4 D39 1304 A 1 HETATM 3 C C5 D39 . . . G 7 104.421 124.818 103.329 1 41.41 ? C5 D39 1304 A 1 HETATM 4 O O4 D39 . . . G 7 105.2 123.813 103.715 1 41.41 ? O4 D39 1304 A 1 HETATM 5 C C6 D39 . . . G 7 103.713 125.423 104.502 1 41.41 ? C6 D39 1304 A 1 HETATM 6 C C7 D39 . . . G 7 104.568 125.433 105.76 1 41.41 ? C7 D39 1304 A 1 HETATM 7 C C8 D39 . . . G 7 103.843 125.986 106.965 1 41.41 ? C8 D39 1304 A 1 HETATM 8 C C9 D39 . . . G 7 102.894 124.998 107.618 1 41.41 ? C9 D39 1304 A 1 HETATM 9 O O5 D39 . . . G 7 104.308 125.174 102.188 1 41.41 ? O5 D39 1304 A 1 HETATM 10 C C10 D39 . . . G 7 101.741 125.661 108.341 1 41.41 ? C10 D39 1304 A 1 HETATM 11 O O6 D39 . . . G 7 105.208 121.131 103.898 1 41.41 ? O6 D39 1304 A 1 HETATM 12 C C11 D39 . . . G 7 101.096 124.815 109.423 1 41.41 ? C11 D39 1304 A 1 HETATM 13 C C12 D39 . . . G 7 99.918 125.499 110.102 1 41.41 ? C12 D39 1304 A 1 HETATM 14 C C13 D39 . . . G 7 100.103 126.994 110.315 1 41.41 ? C13 D39 1304 A 1 HETATM 15 O O7 D39 . . . G 7 106.09 121.137 105.945 1 41.41 ? O7 D39 1304 A 1 HETATM 16 C C14 D39 . . . G 7 99.006 127.652 111.132 1 41.41 ? C14 D39 1304 A 1 HETATM 17 O O8 D39 . . . G 7 111.797 120.049 101.137 1 41.41 ? O8 D39 1304 A 1 HETATM 18 C C15 D39 . . . G 7 99.048 129.182 111.131 1 41.41 ? C15 D39 1304 A 1 HETATM 19 N N D39 . . . G 7 111.032 117.918 99.067 1 41.41 ? N D39 1304 A 1 HETATM 20 C C D39 . . . G 7 110.621 119.32 99.22 1 41.41 ? C D39 1304 A 1 HETATM 21 O O D39 . . . G 7 109.667 119.253 101.433 1 41.41 ? O D39 1304 A 1 HETATM 22 C C1 D39 . . . G 7 109.337 119.382 100.03 1 41.41 ? C1 D39 1304 A 1 HETATM 23 C C16 D39 . . . G 7 98.257 129.808 112.267 1 41.41 ? C16 D39 1304 A 1 HETATM 24 C C17 D39 . . . G 7 98.774 129.403 113.641 1 41.41 ? C17 D39 1304 A 1 HETATM 25 C C18 D39 . . . G 7 97.823 129.709 114.784 1 41.41 ? C18 D39 1304 A 1 HETATM 26 C C19 D39 . . . G 7 96.521 128.948 114.728 1 41.41 ? C19 D39 1304 A 1 HETATM 27 C C2 D39 . . . G 7 107.022 120.89 102.373 1 41.41 ? C2 D39 1304 A 1 HETATM 28 C C20 D39 . . . G 7 95.622 129.239 115.903 1 41.41 ? C20 D39 1304 A 1 HETATM 29 C C21 D39 . . . G 7 105.18 120.897 105.208 1 41.41 ? C21 D39 1304 A 1 HETATM 30 C C22 D39 . . . G 7 103.868 120.316 105.627 1 41.41 ? C22 D39 1304 A 1 HETATM 31 C C23 D39 . . . G 7 103.838 119.922 107.09 1 41.41 ? C23 D39 1304 A 1 HETATM 32 C C24 D39 . . . G 7 102.571 119.219 107.498 1 41.41 ? C24 D39 1304 A 1 HETATM 33 C C25 D39 . . . G 7 101.534 120.147 108.062 1 41.41 ? C25 D39 1304 A 1 HETATM 34 C C26 D39 . . . G 7 100.654 119.503 109.102 1 41.41 ? C26 D39 1304 A 1 HETATM 35 C C27 D39 . . . G 7 99.816 120.491 109.866 1 41.41 ? C27 D39 1304 A 1 HETATM 36 C C28 D39 . . . G 7 98.798 121.229 109.008 1 41.41 ? C28 D39 1304 A 1 HETATM 37 C C29 D39 . . . G 7 98.177 122.381 109.734 1 41.41 ? C29 D39 1304 A 1 HETATM 38 C C3 D39 . . . G 7 106.373 121.813 103.352 1 41.41 ? C3 D39 1304 A 1 HETATM 39 C C30 D39 . . . G 7 97.09 122.346 110.472 1 41.41 ? C30 D39 1304 A 1 HETATM 40 C C31 D39 . . . G 7 96.233 121.151 110.732 1 41.41 ? C31 D39 1304 A 1 HETATM 41 C C32 D39 . . . G 7 95.329 121.336 111.937 1 41.41 ? C32 D39 1304 A 1 HETATM 42 C C33 D39 . . . G 7 93.913 120.845 111.712 1 41.41 ? C33 D39 1304 A 1 HETATM 43 C C34 D39 . . . G 7 93.19 121.556 110.576 1 41.41 ? C34 D39 1304 A 1 HETATM 44 C C35 D39 . . . G 7 91.77 121.068 110.339 1 41.41 ? C35 D39 1304 A 1 HETATM 45 C C36 D39 . . . G 7 90.845 121.244 111.532 1 41.41 ? C36 D39 1304 A 1 HETATM 46 C C37 D39 . . . G 7 90.655 122.682 111.97 1 41.41 ? C37 D39 1304 A 1 HETATM 47 C C38 D39 . . . G 7 89.806 122.819 113.204 1 41.41 ? C38 D39 1304 A 1 HETATM 48 C C39 D39 . . . G 7 111.718 120.176 99.845 1 41.41 ? C39 D39 1304 A 1 HETATM 49 O O1 D39 . . . G 7 107.528 118.118 101.623 1 41.41 ? O1 D39 1304 A 1 HETATM 50 O O2 D39 . . . G 7 109.079 117.875 103.543 1 41.41 ? O2 D39 1304 A 1 HETATM 51 O O9 D39 . . . G 7 112.437 120.894 99.183 1 41.41 ? O9 D39 1304 A 1 HETATM 52 P P D39 . . . G 7 108.572 118.75 102.487 1 41.41 ? P D39 1304 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 389 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 52 #