data_6KKU # _model_server_result.job_id RtrACsiSAgrBU-JxpNsYKA _model_server_result.datetime_utc '2024-12-23 10:30:18' _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 6kku # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1106}' # _entry.id 6KKU # _exptl.entry_id 6KKU _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 516.752 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol" _entity.pdbx_number_of_molecules 2 _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 6KKU _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KKU _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,J,K,L,M,N _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 ? 5 L N N ? 5 N N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 GLC BGC 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 2 n C NAG 1 C 1 NAG A 1102 NAG 2 n C NAG 2 C 2 NAG A 1101 NAG 2 n D NAG 1 D 1 NAG A 1104 NAG 2 n D NAG 2 D 2 NAG A 1103 NAG 3 n E BGC 1 E 1 BGC A 1107 BGC 3 n E GLC 2 E 2 GLC A 1108 GLC 3 n F BGC 1 F 1 BGC A 1109 BGC 3 n F GLC 2 F 2 GLC A 1110 GLC 2 n G NAG 1 G 1 NAG B 1102 NAG 2 n G NAG 2 G 2 NAG B 1101 NAG 2 n H NAG 1 H 1 NAG B 1104 NAG 2 n H NAG 2 H 2 NAG B 1103 NAG 3 n I BGC 1 I 1 BGC B 1106 BGC 3 n I GLC 2 I 2 GLC B 1107 GLC 3 n J BGC 1 J 1 BGC B 1109 BGC 3 n J GLC 2 J 2 GLC B 1110 GLC # 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 A SG CYS 163 A CYS 163 1_555 A SG CYS 626 A CYS 626 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 308 A CYS 308 1_555 A SG CYS 323 A CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 343 A CYS 343 1_555 A SG CYS 353 A CYS 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 B SG CYS 163 B CYS 163 1_555 B SG CYS 626 B CYS 626 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 B SG CYS 308 B CYS 308 1_555 B SG CYS 323 B CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 B SG CYS 343 B CYS 343 1_555 B SG CYS 353 B CYS 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A ND2 ASN 312 A ASN 312 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale2 A ND2 ASN 361 A ASN 361 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale3 L O52 DU0 . A DU0 1106 1_555 E C1 BGC . E BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? covale ? covale4 L O28 DU0 . A DU0 1106 1_555 I C1 BGC . I BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale5 B ND2 ASN 312 B ASN 312 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale6 B ND2 ASN 361 B ASN 361 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale7 N O52 DU0 . B DU0 1108 1_555 F C1 BGC . F BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale8 N O28 DU0 . B DU0 1108 1_555 J C1 BGC . J BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale11 E O4 BGC . E BGC 1 1_555 E C1 GLC . E GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.368 ? covale ? covale12 F O4 BGC . F BGC 1 1_555 F C1 GLC . F GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? covale ? covale13 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale14 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale15 I O4 BGC . I BGC 1 1_555 I C1 GLC . I GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? covale ? covale16 J O4 BGC . J BGC 1 1_555 J C1 GLC . J GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.368 ? # _chem_comp.formula 'C32 H52 O5' _chem_comp.formula_weight 516.752 _chem_comp.id DU0 _chem_comp.mon_nstd_flag . _chem_comp.name "2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol" _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 C13 C12 DU0 sing 107 n n C12 C11 DU0 sing 108 n n C12 C14 DU0 sing 109 n n C11 O10 DU0 sing 110 n n C14 C15 DU0 sing 111 n n O10 C09 DU0 sing 112 n n C15 C09 DU0 sing 113 n n C09 O16 DU0 sing 114 n n C09 C07 DU0 sing 115 n n C08 C07 DU0 sing 116 n n O16 C05 DU0 sing 117 n n C07 C06 DU0 sing 118 n n C05 C06 DU0 sing 119 n n C05 C04 DU0 sing 120 n n C06 C02 DU0 sing 121 n n C04 C03 DU0 sing 122 n n C02 C01 DU0 sing 123 n n C02 C03 DU0 sing 124 n n C02 C81 DU0 sing 125 n n C03 C17 DU0 sing 126 n n C81 C80 DU0 sing 127 n n C17 C18 DU0 sing 128 n n C17 C79 DU0 sing 129 n n C80 C79 DU0 sing 130 n n C18 C19 DU0 sing 131 n n C79 C77 DU0 sing 132 n n C19 C20 DU0 doub 133 n n C77 C20 DU0 sing 134 n n C77 C78 DU0 sing 135 n n C77 C76 DU0 sing 136 n n C20 C21 DU0 sing 137 n n C76 C75 DU0 sing 138 n n C21 C22 DU0 sing 139 n n C75 C22 DU0 sing 140 n n C22 O23 DU0 sing 141 n n O23 C24 DU0 sing 142 n n C24 C25 DU0 sing 143 n n C25 C26 DU0 sing 144 n n C26 C27 DU0 sing 145 n n C26 C51 DU0 sing 146 n n C27 O28 DU0 sing 147 n n C51 O52 DU0 sing 148 n n C13 H1 DU0 sing 149 n n C13 H2 DU0 sing 150 n n C13 H3 DU0 sing 151 n n C15 H4 DU0 sing 152 n n C15 H5 DU0 sing 153 n n C17 H6 DU0 sing 154 n n C21 H7 DU0 sing 155 n n C21 H8 DU0 sing 156 n n C22 H9 DU0 sing 157 n n C24 H10 DU0 sing 158 n n C24 H11 DU0 sing 159 n n C26 H12 DU0 sing 160 n n C01 H13 DU0 sing 161 n n C01 H14 DU0 sing 162 n n C01 H15 DU0 sing 163 n n C03 H16 DU0 sing 164 n n C04 H17 DU0 sing 165 n n C04 H18 DU0 sing 166 n n C05 H19 DU0 sing 167 n n C06 H20 DU0 sing 168 n n C07 H21 DU0 sing 169 n n C08 H22 DU0 sing 170 n n C08 H23 DU0 sing 171 n n C08 H24 DU0 sing 172 n n C11 H25 DU0 sing 173 n n C11 H26 DU0 sing 174 n n C12 H27 DU0 sing 175 n n C14 H28 DU0 sing 176 n n C14 H29 DU0 sing 177 n n C18 H30 DU0 sing 178 n n C18 H31 DU0 sing 179 n n C19 H32 DU0 sing 180 n n C25 H33 DU0 sing 181 n n C25 H34 DU0 sing 182 n n C27 H35 DU0 sing 183 n n C27 H36 DU0 sing 184 n n C51 H37 DU0 sing 185 n n C51 H38 DU0 sing 186 n n C75 H39 DU0 sing 187 n n C75 H40 DU0 sing 188 n n C76 H41 DU0 sing 189 n n C76 H42 DU0 sing 190 n n C78 H43 DU0 sing 191 n n C78 H44 DU0 sing 192 n n C78 H45 DU0 sing 193 n n C79 H46 DU0 sing 194 n n C80 H47 DU0 sing 195 n n C80 H48 DU0 sing 196 n n C81 H49 DU0 sing 197 n n C81 H50 DU0 sing 198 n n O28 H51 DU0 sing 199 n n O52 H52 DU0 sing 200 n n # _atom_sites.entry_id 6KKU _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 K 4 CL A 1 1105 1105 CL CL . L 5 DU0 A 1 1106 1106 DU0 DU0 . M 4 CL B 1 1105 1105 CL CL . N 5 DU0 B 1 1108 1108 DU0 DU0 . # 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 C13 DU0 . . . L 5 114.029 104.628 101.496 1 30 ? C13 DU0 1106 A 1 HETATM 2 C C15 DU0 . . . L 5 116.769 104.638 104.106 1 30 ? C15 DU0 1106 A 1 HETATM 3 C C17 DU0 . . . L 5 114.404 107.006 109.968 1 30 ? C17 DU0 1106 A 1 HETATM 4 C C20 DU0 . . . L 5 113.651 107.62 112.669 1 30 ? C20 DU0 1106 A 1 HETATM 5 C C21 DU0 . . . L 5 113.337 107.661 114.151 1 30 ? C21 DU0 1106 A 1 HETATM 6 C C22 DU0 . . . L 5 113.869 108.94 114.789 1 30 ? C22 DU0 1106 A 1 HETATM 7 C C24 DU0 . . . L 5 112.527 109.72 116.54 1 30 ? C24 DU0 1106 A 1 HETATM 8 C C26 DU0 . . . L 5 113.09 108.523 118.741 1 30 ? C26 DU0 1106 A 1 HETATM 9 C C01 DU0 . . . L 5 116.815 105.782 108.349 1 30 ? C01 DU0 1106 A 1 HETATM 10 C C02 DU0 . . . L 5 116.119 107.116 108.026 1 30 ? C02 DU0 1106 A 1 HETATM 11 C C03 DU0 . . . L 5 114.642 107.178 108.466 1 30 ? C03 DU0 1106 A 1 HETATM 12 C C04 DU0 . . . L 5 113.951 106.209 107.508 1 30 ? C04 DU0 1106 A 1 HETATM 13 C C05 DU0 . . . L 5 114.633 106.592 106.196 1 30 ? C05 DU0 1106 A 1 HETATM 14 C C06 DU0 . . . L 5 115.931 107.339 106.511 1 30 ? C06 DU0 1106 A 1 HETATM 15 C C07 DU0 . . . L 5 116.93 106.748 105.507 1 30 ? C07 DU0 1106 A 1 HETATM 16 C C08 DU0 . . . L 5 117.81 107.795 104.815 1 30 ? C08 DU0 1106 A 1 HETATM 17 C C09 DU0 . . . L 5 116.051 105.889 104.6 1 30 ? C09 DU0 1106 A 1 HETATM 18 C C11 DU0 . . . L 5 115.7 106.346 102.25 1 30 ? C11 DU0 1106 A 1 HETATM 19 C C12 DU0 . . . L 5 115.486 104.873 101.911 1 30 ? C12 DU0 1106 A 1 HETATM 20 C C14 DU0 . . . L 5 115.919 103.927 103.046 1 30 ? C14 DU0 1106 A 1 HETATM 21 C C18 DU0 . . . L 5 112.922 107.21 110.303 1 30 ? C18 DU0 1106 A 1 HETATM 22 C C19 DU0 . . . L 5 112.692 107.32 111.78 1 30 ? C19 DU0 1106 A 1 HETATM 23 C C25 DU0 . . . L 5 112.395 109.701 118.062 1 30 ? C25 DU0 1106 A 1 HETATM 24 C C27 DU0 . . . L 5 114.632 108.839 118.932 1 30 ? C27 DU0 1106 A 1 HETATM 25 C C51 DU0 . . . L 5 112.322 107.808 119.944 1 30 ? C51 DU0 1106 A 1 HETATM 26 C C75 DU0 . . . L 5 115.366 109.041 114.522 1 30 ? C75 DU0 1106 A 1 HETATM 27 C C76 DU0 . . . L 5 115.635 109.046 113.014 1 30 ? C76 DU0 1106 A 1 HETATM 28 C C77 DU0 . . . L 5 115.109 107.798 112.28 1 30 ? C77 DU0 1106 A 1 HETATM 29 C C78 DU0 . . . L 5 115.896 106.556 112.727 1 30 ? C78 DU0 1106 A 1 HETATM 30 C C79 DU0 . . . L 5 115.253 108.021 110.753 1 30 ? C79 DU0 1106 A 1 HETATM 31 C C80 DU0 . . . L 5 116.712 108.047 110.268 1 30 ? C80 DU0 1106 A 1 HETATM 32 C C81 DU0 . . . L 5 116.84 108.252 108.751 1 30 ? C81 DU0 1106 A 1 HETATM 33 O O10 DU0 . . . L 5 115.403 106.641 103.59 1 30 ? O10 DU0 1106 A 1 HETATM 34 O O16 DU0 . . . L 5 115.007 105.482 105.447 1 30 ? O16 DU0 1106 A 1 HETATM 35 O O23 DU0 . . . L 5 113.591 108.892 116.16 1 30 ? O23 DU0 1106 A 1 HETATM 36 O O28 DU0 . . . L 5 114.754 109.6 120.068 1 30 ? O28 DU0 1106 A 1 HETATM 37 O O52 DU0 . . . L 5 112.588 108.398 121.207 1 30 ? O52 DU0 1106 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 37 #