data_9BVM # _model_server_result.job_id DnBRWJGfL70BCm2tMyt7IQ _model_server_result.datetime_utc '2025-02-19 02:13:34' _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 9bvm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":801}' # _entry.id 9BVM # _exptl.entry_id 9BVM _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 452.712 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'vitamin K1 hydroquinone' _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 9BVM _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9BVM _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_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 _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 x,y,z _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 4 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 B 1 NAG 3 n C NAG 2 B 2 NAG B 2 NAG 3 n D NAG 1 C 1 NAG C 1 NAG 3 n D NAG 2 C 2 NAG C 2 NAG 3 n E NAG 1 D 1 NAG D 1 NAG 3 n E NAG 2 D 2 NAG D 2 NAG # 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 73 A CYS 99 1_555 A SG CYS 424 A CYS 450 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 433 A ASN 459 1_555 I C1 NAG . A NAG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.502 ? covale ? covale2 A ND2 ASN 544 A ASN 570 1_555 C C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 A ND2 ASN 579 A ASN 605 1_555 E C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 C O4 NAG . B NAG 1 1_555 C C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 D O4 NAG . C NAG 1 1_555 D C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.173 ? covale ? covale6 E O4 NAG . D NAG 1 1_555 E C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? # _chem_comp.formula 'C31 H48 O2' _chem_comp.formula_weight 452.712 _chem_comp.id A1AVC _chem_comp.mon_nstd_flag . _chem_comp.name 'vitamin K1 hydroquinone' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 2-methyl-3-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]naphthalene-1,4-diol # 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 C30 C29 A1AVC sing 137 n n C29 C28 A1AVC sing 138 n n C29 C31 A1AVC sing 139 n n C28 C27 A1AVC sing 140 n n C21 C22 A1AVC sing 141 n n C21 C19 A1AVC sing 142 n n C18 C17 A1AVC sing 143 n n C18 C19 A1AVC sing 144 n n C16 C17 A1AVC sing 145 n n C16 C14 A1AVC sing 146 n n C27 C26 A1AVC sing 147 n n C15 C14 A1AVC sing 148 n n C22 C23 A1AVC sing 149 n n C14 C13 A1AVC doub 150 e n C19 C20 A1AVC sing 151 n n C26 C24 A1AVC sing 152 n n C23 C24 A1AVC sing 153 n n C13 C12 A1AVC sing 154 n n C24 C25 A1AVC sing 155 n n C12 C11 A1AVC sing 156 n n O32 C10 A1AVC sing 157 n n C11 C10 A1AVC doub 158 n y C11 C02 A1AVC sing 159 n y C01 C02 A1AVC sing 160 n n C10 C09 A1AVC sing 161 n y C02 C03 A1AVC doub 162 n y C09 C08 A1AVC sing 163 n y C09 C04 A1AVC doub 164 n y C03 C04 A1AVC sing 165 n y C03 O33 A1AVC sing 166 n n C08 C07 A1AVC doub 167 n y C04 C05 A1AVC sing 168 n y C07 C06 A1AVC sing 169 n y C05 C06 A1AVC doub 170 n y C12 H1 A1AVC sing 171 n n C12 H2 A1AVC sing 172 n n C13 H3 A1AVC sing 173 n n C15 H4 A1AVC sing 174 n n C15 H5 A1AVC sing 175 n n C15 H6 A1AVC sing 176 n n C16 H7 A1AVC sing 177 n n C16 H8 A1AVC sing 178 n n C01 H9 A1AVC sing 179 n n C01 H10 A1AVC sing 180 n n C01 H11 A1AVC sing 181 n n C05 H12 A1AVC sing 182 n n C06 H13 A1AVC sing 183 n n C07 H14 A1AVC sing 184 n n C08 H15 A1AVC sing 185 n n C17 H16 A1AVC sing 186 n n C17 H17 A1AVC sing 187 n n C18 H18 A1AVC sing 188 n n C18 H19 A1AVC sing 189 n n C19 H20 A1AVC sing 190 n n C20 H21 A1AVC sing 191 n n C20 H22 A1AVC sing 192 n n C20 H23 A1AVC sing 193 n n C21 H24 A1AVC sing 194 n n C21 H25 A1AVC sing 195 n n C22 H26 A1AVC sing 196 n n C22 H27 A1AVC sing 197 n n C23 H28 A1AVC sing 198 n n C23 H29 A1AVC sing 199 n n C24 H30 A1AVC sing 200 n n C25 H31 A1AVC sing 201 n n C25 H32 A1AVC sing 202 n n C25 H33 A1AVC sing 203 n n C26 H34 A1AVC sing 204 n n C26 H35 A1AVC sing 205 n n C27 H36 A1AVC sing 206 n n C27 H37 A1AVC sing 207 n n C28 H38 A1AVC sing 208 n n C28 H39 A1AVC sing 209 n n C29 H40 A1AVC sing 210 n n C30 H41 A1AVC sing 211 n n C30 H42 A1AVC sing 212 n n C30 H43 A1AVC sing 213 n n C31 H44 A1AVC sing 214 n n C31 H45 A1AVC sing 215 n n C31 H46 A1AVC sing 216 n n O32 H47 A1AVC sing 217 n n O33 H48 A1AVC sing 218 n n # _atom_sites.entry_id 9BVM _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 F 4 A1AVC A 1 801 801 A1AVC KH2 . G 5 6PL A 1 802 802 6PL 6PL . H 5 6PL A 1 803 803 6PL 6PL . I 6 NAG A 1 804 13 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 C C11 A1AVC . . . F 4 146.642 142.24 135.493 1 73.61 ? C11 A1AVC 801 A 1 HETATM 2 C C12 A1AVC . . . F 4 147.762 142.888 134.629 1 71.76 ? C12 A1AVC 801 A 1 HETATM 3 C C13 A1AVC . . . F 4 147.709 142.187 133.239 1 71.49 ? C13 A1AVC 801 A 1 HETATM 4 C C14 A1AVC . . . F 4 148.769 141.567 132.629 1 71.77 ? C14 A1AVC 801 A 1 HETATM 5 C C15 A1AVC . . . F 4 150.173 141.5 133.259 1 71.56 ? C15 A1AVC 801 A 1 HETATM 6 C C16 A1AVC . . . F 4 148.554 140.908 131.226 1 69.08 ? C16 A1AVC 801 A 1 HETATM 7 C C01 A1AVC . . . F 4 148.333 140.877 136.911 1 72.89 ? C01 A1AVC 801 A 1 HETATM 8 C C02 A1AVC . . . F 4 146.882 141.323 136.532 1 74.86 ? C02 A1AVC 801 A 1 HETATM 9 C C03 A1AVC . . . F 4 145.781 140.79 137.247 1 69.19 ? C03 A1AVC 801 A 1 HETATM 10 C C04 A1AVC . . . F 4 144.433 141.183 136.913 1 72.43 ? C04 A1AVC 801 A 1 HETATM 11 C C05 A1AVC . . . F 4 143.329 140.637 137.646 1 69.47 ? C05 A1AVC 801 A 1 HETATM 12 C C06 A1AVC . . . F 4 142.017 141.019 137.323 1 69.19 ? C06 A1AVC 801 A 1 HETATM 13 C C07 A1AVC . . . F 4 141.783 141.931 136.288 1 68.38 ? C07 A1AVC 801 A 1 HETATM 14 C C08 A1AVC . . . F 4 142.86 142.464 135.572 1 70.48 ? C08 A1AVC 801 A 1 HETATM 15 C C09 A1AVC . . . F 4 144.205 142.07 135.906 1 74.76 ? C09 A1AVC 801 A 1 HETATM 16 C C10 A1AVC . . . F 4 145.306 142.614 135.177 1 72.29 ? C10 A1AVC 801 A 1 HETATM 17 C C17 A1AVC . . . F 4 148.814 139.344 131.278 1 72.58 ? C17 A1AVC 801 A 1 HETATM 18 C C18 A1AVC . . . F 4 149.773 138.798 130.154 1 72.19 ? C18 A1AVC 801 A 1 HETATM 19 C C19 A1AVC . . . F 4 149.081 138.08 128.994 1 73.23 ? C19 A1AVC 801 A 1 HETATM 20 C C20 A1AVC . . . F 4 147.971 138.955 128.386 1 70.15 ? C20 A1AVC 801 A 1 HETATM 21 C C21 A1AVC . . . F 4 148.512 136.707 129.433 1 73.94 ? C21 A1AVC 801 A 1 HETATM 22 C C22 A1AVC . . . F 4 148.316 135.779 128.189 1 75.88 ? C22 A1AVC 801 A 1 HETATM 23 C C23 A1AVC . . . F 4 147.072 134.865 128.24 1 78.94 ? C23 A1AVC 801 A 1 HETATM 24 C C24 A1AVC . . . F 4 145.901 135.274 127.297 1 83.08 ? C24 A1AVC 801 A 1 HETATM 25 C C25 A1AVC . . . F 4 144.715 134.354 127.56 1 76.79 ? C25 A1AVC 801 A 1 HETATM 26 C C26 A1AVC . . . F 4 146.307 135.157 125.826 1 81.81 ? C26 A1AVC 801 A 1 HETATM 27 C C27 A1AVC . . . F 4 145.128 135.179 124.809 1 82.64 ? C27 A1AVC 801 A 1 HETATM 28 C C28 A1AVC . . . F 4 145.636 135.562 123.392 1 82.6 ? C28 A1AVC 801 A 1 HETATM 29 C C29 A1AVC . . . F 4 144.882 134.871 122.252 1 86.48 ? C29 A1AVC 801 A 1 HETATM 30 C C30 A1AVC . . . F 4 145.185 133.348 122.191 1 82.74 ? C30 A1AVC 801 A 1 HETATM 31 C C31 A1AVC . . . F 4 145.206 135.526 120.929 1 80.69 ? C31 A1AVC 801 A 1 HETATM 32 O O32 A1AVC . . . F 4 145.062 143.525 134.143 1 69.13 ? O32 A1AVC 801 A 1 HETATM 33 O O33 A1AVC . . . F 4 145.969 139.876 138.287 1 65.35 ? O33 A1AVC 801 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 948 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 33 #