data_6EJK # _model_server_result.job_id F8Jnp0FvPxyRnaucIKJfLQ _model_server_result.datetime_utc '2024-11-24 12:12:21' _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 6ejk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":405}' # _entry.id 6EJK # _exptl.entry_id 6EJK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 450.443 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NerylNeryl pyrophosphate' _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 90.27 _cell.angle_gamma 90 _cell.entry_id 6EJK _cell.length_a 60.87 _cell.length_b 126.91 _cell.length_c 71.09 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6EJK _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F 1 1 B,D,G,H 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 H N N # _pdbx_entity_branch.entity_id 2 _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 ? 2 2 1 A2G NDG C1 O1 . O3 HO3 . sing 2 ? 2 3 2 A2G A2G 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 NDG 1 C 1 NDG A 404 NDG 2 n C A2G 2 C 2 A2G A 403 A2G 2 n C A2G 3 C 3 A2G A 402 A2G 2 n D NDG 1 D 1 NDG B 404 NDG 2 n D A2G 2 D 2 A2G B 403 A2G 2 n D A2G 3 D 3 A2G B 402 A2G # 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 covale ? covale1 A C MSE 1 A MSE 1 1_555 A N MSE 2 A MSE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale2 A C MSE 2 A MSE 2 1_555 A N MSE 3 A MSE 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 A C MSE 3 A MSE 3 1_555 A N LYS 4 A LYS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale4 A C VAL 199 A VAL 199 1_555 A N MSE 200 A MSE 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale5 A C MSE 200 A MSE 200 1_555 A N PHE 201 A PHE 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 F O36 BUE . A BUE 405 1_555 C C1 NDG . C NDG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale7 B C MSE 1 B MSE 1 1_555 B N MSE 2 B MSE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale8 B C MSE 2 B MSE 2 1_555 B N MSE 3 B MSE 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale9 B C MSE 3 B MSE 3 1_555 B N LYS 4 B LYS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? covale ? covale10 B C VAL 199 B VAL 199 1_555 B N MSE 200 B MSE 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale11 B C MSE 200 B MSE 200 1_555 B N PHE 201 B PHE 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale12 H O36 BUE . B BUE 405 1_555 D C1 NDG . D NDG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? covale ? covale13 C O3 NDG . C NDG 1 1_555 C C1 A2G . C A2G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.373 ? covale ? covale14 C O4 A2G . C A2G 2 1_555 C C1 A2G . C A2G 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale15 D O3 NDG . D NDG 1 1_555 D C1 A2G . D A2G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.371 ? covale ? covale16 D O4 A2G . D A2G 2 1_555 D C1 A2G . D A2G 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? # _chem_comp.formula 'C20 H36 O7 P2' _chem_comp.formula_weight 450.443 _chem_comp.id BUE _chem_comp.mon_nstd_flag . _chem_comp.name 'NerylNeryl pyrophosphate' _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 O34 P35 BUE doub 100 n n O36 P35 BUE sing 101 n n P35 O38 BUE sing 102 n n P35 O37 BUE sing 103 n n O38 P39 BUE sing 104 n n O42 P39 BUE sing 105 n n O42 C43 BUE sing 106 n n O41 P39 BUE doub 107 n n P39 O40 BUE sing 108 n n C43 C44 BUE sing 109 n n O36 H1 BUE sing 110 n n O37 H2 BUE sing 111 n n O40 H3 BUE sing 112 n n C43 H4 BUE sing 113 n n C43 H5 BUE sing 114 n n C44 H6 BUE sing 115 n n C44 C1 BUE doub 116 n n C1 C2 BUE sing 117 n n C1 C15 BUE sing 118 n n C2 H7 BUE sing 119 n n C2 H8 BUE sing 120 n n C15 H25 BUE sing 121 n n C15 H26 BUE sing 122 n n C15 C19 BUE sing 123 n n C19 C20 BUE sing 124 n n C20 C21 BUE doub 125 n n C21 C22 BUE sing 126 n n C21 C3 BUE sing 127 n n C2 H9 BUE sing 128 n n C19 H10 BUE sing 129 n n C19 H11 BUE sing 130 n n C20 H12 BUE sing 131 n n C22 H13 BUE sing 132 n n C22 H14 BUE sing 133 n n C22 H15 BUE sing 134 n n C3 H16 BUE sing 135 n n C3 H17 BUE sing 136 n n C3 C4 BUE sing 137 n n C4 C5 BUE sing 138 n n C5 C6 BUE doub 139 n n C6 C7 BUE sing 140 n n C6 C8 BUE sing 141 n n C4 H18 BUE sing 142 n n C4 H19 BUE sing 143 n n C5 H20 BUE sing 144 n n C7 H21 BUE sing 145 n n C7 H22 BUE sing 146 n n C7 H23 BUE sing 147 n n C8 H24 BUE sing 148 n n C8 H27 BUE sing 149 n n C8 C9 BUE sing 150 n n C9 C10 BUE sing 151 n n C10 C11 BUE doub 152 n n C11 C12 BUE sing 153 n n C11 C13 BUE sing 154 n n C9 H28 BUE sing 155 n n C9 H29 BUE sing 156 n n C10 H30 BUE sing 157 n n C12 H31 BUE sing 158 n n C12 H32 BUE sing 159 n n C12 H33 BUE sing 160 n n C13 H34 BUE sing 161 n n C13 H35 BUE sing 162 n n C13 H36 BUE sing 163 n n # _atom_sites.entry_id 6EJK _atom_sites.fract_transf_matrix[1][1] 0.016428 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000076 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00788 _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] 0.014067 _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 3 UDN A 1 401 401 UDN UDN . F 4 BUE A 1 405 405 BUE BUE . G 3 UDN B 1 401 401 UDN UDN . H 4 BUE B 1 405 405 BUE BUE . # 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 O34 BUE . . . F 4 73.294 -23.257 26.741 1 131.84 ? O34 BUE 405 A 1 HETATM 2 P P35 BUE . . . F 4 73.758 -22.344 27.788 1 131.03 ? P35 BUE 405 A 1 HETATM 3 O O36 BUE . . . F 4 73.562 -20.758 27.275 1 128.69 ? O36 BUE 405 A 1 HETATM 4 O O37 BUE . . . F 4 72.75 -22.696 28.795 1 132.55 ? O37 BUE 405 A 1 HETATM 5 O O38 BUE . . . F 4 75.323 -22.761 28.3 1 131.8 ? O38 BUE 405 A 1 HETATM 6 P P39 BUE . . . F 4 76.372 -22.045 29.418 1 131.7 ? P39 BUE 405 A 1 HETATM 7 O O40 BUE . . . F 4 76.066 -22.395 30.812 1 133.53 ? O40 BUE 405 A 1 HETATM 8 O O41 BUE . . . F 4 77.691 -22.658 29.35 1 132.88 ? O41 BUE 405 A 1 HETATM 9 O O42 BUE . . . F 4 76.491 -20.41 29.17 1 129.23 ? O42 BUE 405 A 1 HETATM 10 C C43 BUE . . . F 4 77.642 -19.752 29.604 1 128.98 ? C43 BUE 405 A 1 HETATM 11 C C44 BUE . . . F 4 77.569 -19.668 31.121 1 130.19 ? C44 BUE 405 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 11 #