data_6EJJ # _model_server_result.job_id ZKN5LhytKCuOcCepYciE9A _model_server_result.datetime_utc '2024-11-23 23:21:45' _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 6ejj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":408}' # _entry.id 6EJJ # _exptl.entry_id 6EJJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 450.443 _entity.id 6 _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 90.28 _cell.angle_gamma 90 _cell.entry_id 6EJJ _cell.length_a 60.51 _cell.length_b 125.78 _cell.length_c 71.01 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6EJJ _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,G,H,I,N 1 1 B,D,J,K,L,M,O 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 ? 6 I N N ? 6 M 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 C 1 LLO 2 n C A2G 2 C 2 A2G C 1 LLO 2 n C A2G 3 C 3 A2G C 1 LLO 2 n D NDG 1 D 1 NDG C 2 LLO 2 n D A2G 2 D 2 A2G C 2 LLO 2 n D A2G 3 D 3 A2G C 2 LLO # 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 I O34 BUE . A BUE 408 1_555 C C1 NDG . C NDG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale2 M O36 BUE . B BUE 407 1_555 D C1 NDG . D NDG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale3 C O3 NDG . C NDG 1 1_555 C C1 A2G . C A2G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? covale ? covale4 C O4 A2G . C A2G 2 1_555 C C1 A2G . C A2G 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale5 D O3 NDG . D NDG 1 1_555 D C1 A2G . D A2G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? covale ? covale6 D O4 A2G . D A2G 2 1_555 D C1 A2G . D A2G 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? metalc ? metalc1 A OE2 GLU 267 A GLU 267 1_555 G NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? metalc ? metalc2 F NA NA . A NA 402 1_555 I O36 BUE . A BUE 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? metalc ? metalc3 F NA NA . A NA 402 1_555 I O37 BUE . A BUE 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? metalc ? metalc4 F NA NA . A NA 402 1_555 N O HOH . A HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc5 B O ILE 189 B ILE 189 1_555 K NA NA . B NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.07 ? metalc ? metalc6 J O2A UDP . B UDP 401 1_555 K NA NA . B NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc7 L NA NA . B NA 403 1_555 M O34 BUE . B BUE 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.803 ? metalc ? metalc8 L NA NA . B NA 403 1_555 M O37 BUE . B BUE 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? # _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 6EJJ _atom_sites.fract_transf_matrix[1][1] 0.016526 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000082 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00795 _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] 0.014083 _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 UDP A 1 401 1 UDP LIG . F 4 NA A 1 402 3 NA NA . G 4 NA A 1 403 6 NA NA . H 5 CL A 1 404 1 CL CL . I 6 BUE A 1 408 1 BUE LLO . J 3 UDP B 1 401 2 UDP LIG . K 4 NA B 1 402 4 NA NA . L 4 NA B 1 403 5 NA NA . M 6 BUE B 1 407 2 BUE LLO . N 7 HOH A 1 501 18 HOH HOH . N 7 HOH A 2 502 54 HOH HOH . N 7 HOH A 3 503 72 HOH HOH . N 7 HOH A 4 504 67 HOH HOH . N 7 HOH A 5 505 4 HOH HOH . N 7 HOH A 6 506 21 HOH HOH . N 7 HOH A 7 507 16 HOH HOH . N 7 HOH A 8 508 66 HOH HOH . N 7 HOH A 9 509 70 HOH HOH . N 7 HOH A 10 510 69 HOH HOH . N 7 HOH A 11 511 40 HOH HOH . N 7 HOH A 12 512 57 HOH HOH . N 7 HOH A 13 513 73 HOH HOH . N 7 HOH A 14 514 48 HOH HOH . N 7 HOH A 15 515 56 HOH HOH . N 7 HOH A 16 516 63 HOH HOH . N 7 HOH A 17 517 51 HOH HOH . N 7 HOH A 18 518 19 HOH HOH . N 7 HOH A 19 519 68 HOH HOH . N 7 HOH A 20 520 3 HOH HOH . N 7 HOH A 21 521 5 HOH HOH . N 7 HOH A 22 522 7 HOH HOH . N 7 HOH A 23 523 6 HOH HOH . N 7 HOH A 24 524 71 HOH HOH . N 7 HOH A 25 525 65 HOH HOH . O 7 HOH B 1 501 38 HOH HOH . O 7 HOH B 2 502 53 HOH HOH . O 7 HOH B 3 503 37 HOH HOH . O 7 HOH B 4 504 62 HOH HOH . O 7 HOH B 5 505 29 HOH HOH . O 7 HOH B 6 506 35 HOH HOH . O 7 HOH B 7 507 2 HOH HOH . O 7 HOH B 8 508 30 HOH HOH . O 7 HOH B 9 509 23 HOH HOH . O 7 HOH B 10 510 20 HOH HOH . O 7 HOH B 11 511 17 HOH HOH . O 7 HOH B 12 512 12 HOH HOH . O 7 HOH B 13 513 75 HOH HOH . O 7 HOH B 14 514 52 HOH HOH . O 7 HOH B 15 515 1 HOH HOH . O 7 HOH B 16 516 13 HOH HOH . O 7 HOH B 17 517 43 HOH HOH . O 7 HOH B 18 518 22 HOH HOH . O 7 HOH B 19 519 42 HOH HOH . O 7 HOH B 20 520 74 HOH HOH . # 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 . . . I 6 71.705 19.607 26.216 1 72.98 ? O34 BUE 408 A 1 HETATM 2 P P35 BUE . . . I 6 71.237 20.944 27.117 1 75.43 ? P35 BUE 408 A 1 HETATM 3 O O36 BUE . . . I 6 71.856 22.16 26.587 1 74.96 ? O36 BUE 408 A 1 HETATM 4 O O37 BUE . . . I 6 71.888 20.94 28.433 1 78.21 ? O37 BUE 408 A 1 HETATM 5 O O38 BUE . . . I 6 69.557 21.11 27.232 1 75.78 ? O38 BUE 408 A 1 HETATM 6 P P39 BUE . . . I 6 68.481 20.618 28.446 1 74.32 ? P39 BUE 408 A 1 HETATM 7 O O40 BUE . . . I 6 68.963 20.899 29.799 1 74.08 ? O40 BUE 408 A 1 HETATM 8 O O41 BUE . . . I 6 67.271 21.451 28.466 1 76.25 ? O41 BUE 408 A 1 HETATM 9 O O42 BUE . . . I 6 68.113 19.004 28.282 1 71.27 ? O42 BUE 408 A 1 HETATM 10 C C43 BUE . . . I 6 66.807 18.602 28.002 1 68.95 ? C43 BUE 408 A 1 HETATM 11 C C44 BUE . . . I 6 66.105 18.391 29.333 1 69.5 ? C44 BUE 408 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 11 #